|
GLYLIB
0.3.0b
|
|
GLYLIB
0.3.0b
|
#include <run_control.h>
Public Attributes | |
| int | nclambda |
| The number of clambda values held in this struct. | |
| double * | clambda |
| clambda values (see icfe and klambda) -- an array here b/c they are usually in groups | |
| double | comp |
| The compressibility of a system (default = 44.6);. | |
| double | cut |
| Nonbonded cutoff (default = 8.0);. | |
| double | dielc |
| Dielectric for electrostatics (not same as GB simulations) | |
| double | drms |
| convergence criterion for minimization (see manual) | |
| double | dt |
| Time step (psec) for MD runs (recommended max is 0.0020);. | |
| double | dx0 |
| Initial min step length to use (program will self-adjust) | |
| int | ibelly |
| Belly type dynamics. Default is 0 (don't use). See manual. | |
| int | icfe |
| Flag for thermodynamic integration; no=0; yes=1; (see clambda and klambda) | |
| int | igb |
| Flag for using GB or PB IS models; See Manual. | |
| int | imin |
| no_min=0; min=1; read_traj_and_analyze=5 | |
| int | ioutfm |
| crd & vel output formats; normal=0; NetCDF=1 | |
| int | irest |
| don't_restart=0; restart=1 | |
| int | iwrap |
| don't_wrap=0; wrap=1 | |
| double | klambda |
| klambda value (see icfe and clambda) | |
| int | maxcyc |
| Maximum number of minimization cycles. | |
| int | ncyc |
| at ncyc, switch from steepest descent to conjugate graduent. | |
| int | nmropt |
| none=0; some>0; NOESY=2 | |
| int | nsnb |
| Frequencey of nonbonded list updates (default = 25);. | |
| int | nstlim |
| Number of MD simulation steps. | |
| int | ntave |
| Every ntave steps print averages over last ntave steps; =0 to disable averaging. | |
| int | ntb |
| =1 for const. volume ; =2 for constant pressure ; =0 for no periodicity | |
| int | ntc |
| No Shake = 1; SHAKE=2; constrain all bonds = 3. | |
| int | ntf |
| Set equal to ntc or see manual for more information. | |
| int | ntmin |
| Min Method. See manual. If =1, need to set ncyc for switch. | |
| int | ntp |
| Sets pressure control. | |
| int | ntpr |
| Every ntpr steps, print info to mdinfo and mdout. | |
| int | ntr |
| Sets restraints information; =0 for none; >0 for some (see restraint* & refc) | |
| int | ntrx |
| refc format text=1; binary=0 | |
| int | ntt |
| Sets temperature control Const.Energy=0; >0 is some other control (=1 usually, see manual) | |
| int | ntwe |
| Eery ntwe steps write compact energy to mden file; =0 to inhibit. | |
| int | ntwprt |
| Only print atoms 1 through ntwprt in crd files; =0 to print all. | |
| int | ntwr |
| Every ntwr steps write a restart file. | |
| int | ntwv |
| Every ntwx velocities are written to mdvel; =0 to inhibit; =-1 to combine with crd file. | |
| int | ntwx |
| Every ntwx coordinates are written to mdcrd; =0 to inhibit. | |
| int | ntx |
| only_crd=1; crd+vel=5 | |
| int | ntxo |
| format of restrt file (output); =1 only (=0 is deprecated) | |
| double | pres0 |
| Desired constant pressure (bars); default = 1.0;. | |
| double | presi |
| Initial pressure. | |
| double | restraint_wt |
| Sixe of k, the restraining spring constant. | |
| char * | restraintmask |
| List of atoms to be restrained if ntr=1. | |
| double | scee |
| Divide 1-4 electrostatic interactions by scee ; GLYCAM needs = 1.0;. | |
| double | scnb |
| Divide 1-4 vdW interactions by scnb; GLYCAm needs = 1.0;. | |
| double | taup |
| Pressure relaxation time = 0.1;. | |
| double | tautp |
| Time constant for heat-bath coupling; default = 1.0;. | |
| double | temp0 |
| Desired constant temperature (kelvin) | |
| double | tempi |
| Initial temperature. | |
Contains "cntrl" information pertinent to a sander/pmemd run. Currently, in the interest of time, I'm only writing it to contain the pieces I typically use in a run. The rest can be added later as these structs are easily extensible.
Definition at line 99 of file run_control.h.
| double* sander_pmemd_cntrl::clambda |
clambda values (see icfe and klambda) -- an array here b/c they are usually in groups
Definition at line 102 of file run_control.h.
| double sander_pmemd_cntrl::comp |
The compressibility of a system (default = 44.6);.
Definition at line 103 of file run_control.h.
| double sander_pmemd_cntrl::cut |
Nonbonded cutoff (default = 8.0);.
Definition at line 104 of file run_control.h.
| double sander_pmemd_cntrl::dielc |
Dielectric for electrostatics (not same as GB simulations)
Definition at line 106 of file run_control.h.
| double sander_pmemd_cntrl::drms |
convergence criterion for minimization (see manual)
Definition at line 107 of file run_control.h.
| double sander_pmemd_cntrl::dt |
Time step (psec) for MD runs (recommended max is 0.0020);.
Definition at line 108 of file run_control.h.
| double sander_pmemd_cntrl::dx0 |
Initial min step length to use (program will self-adjust)
Definition at line 109 of file run_control.h.
Belly type dynamics. Default is 0 (don't use). See manual.
Definition at line 111 of file run_control.h.
Flag for thermodynamic integration; no=0; yes=1; (see clambda and klambda)
Definition at line 112 of file run_control.h.
Flag for using GB or PB IS models; See Manual.
Definition at line 113 of file run_control.h.
no_min=0; min=1; read_traj_and_analyze=5
Definition at line 114 of file run_control.h.
crd & vel output formats; normal=0; NetCDF=1
Definition at line 115 of file run_control.h.
don't_restart=0; restart=1
Definition at line 116 of file run_control.h.
don't_wrap=0; wrap=1
Definition at line 117 of file run_control.h.
| double sander_pmemd_cntrl::klambda |
klambda value (see icfe and clambda)
Definition at line 119 of file run_control.h.
Maximum number of minimization cycles.
Definition at line 121 of file run_control.h.
The number of clambda values held in this struct.
Definition at line 101 of file run_control.h.
at ncyc, switch from steepest descent to conjugate graduent.
Definition at line 123 of file run_control.h.
none=0; some>0; NOESY=2
Definition at line 124 of file run_control.h.
Frequencey of nonbonded list updates (default = 25);.
Definition at line 125 of file run_control.h.
Number of MD simulation steps.
Definition at line 126 of file run_control.h.
Every ntave steps print averages over last ntave steps; =0 to disable averaging.
Definition at line 127 of file run_control.h.
=1 for const. volume ; =2 for constant pressure ; =0 for no periodicity
Definition at line 128 of file run_control.h.
No Shake = 1; SHAKE=2; constrain all bonds = 3.
Definition at line 129 of file run_control.h.
Set equal to ntc or see manual for more information.
Definition at line 130 of file run_control.h.
Min Method. See manual. If =1, need to set ncyc for switch.
Definition at line 131 of file run_control.h.
Sets pressure control.
Definition at line 132 of file run_control.h.
Every ntpr steps, print info to mdinfo and mdout.
Definition at line 133 of file run_control.h.
Sets restraints information; =0 for none; >0 for some (see restraint* & refc)
Definition at line 134 of file run_control.h.
refc format text=1; binary=0
Definition at line 135 of file run_control.h.
Sets temperature control Const.Energy=0; >0 is some other control (=1 usually, see manual)
Definition at line 136 of file run_control.h.
Eery ntwe steps write compact energy to mden file; =0 to inhibit.
Definition at line 137 of file run_control.h.
Only print atoms 1 through ntwprt in crd files; =0 to print all.
Definition at line 138 of file run_control.h.
Every ntwr steps write a restart file.
Definition at line 139 of file run_control.h.
Every ntwx velocities are written to mdvel; =0 to inhibit; =-1 to combine with crd file.
Definition at line 140 of file run_control.h.
Every ntwx coordinates are written to mdcrd; =0 to inhibit.
Definition at line 141 of file run_control.h.
only_crd=1; crd+vel=5
Definition at line 142 of file run_control.h.
format of restrt file (output); =1 only (=0 is deprecated)
Definition at line 143 of file run_control.h.
| double sander_pmemd_cntrl::pres0 |
Desired constant pressure (bars); default = 1.0;.
Definition at line 145 of file run_control.h.
| double sander_pmemd_cntrl::presi |
Initial pressure.
Definition at line 146 of file run_control.h.
Sixe of k, the restraining spring constant.
Definition at line 148 of file run_control.h.
List of atoms to be restrained if ntr=1.
Definition at line 149 of file run_control.h.
| double sander_pmemd_cntrl::scee |
Divide 1-4 electrostatic interactions by scee ; GLYCAM needs = 1.0;.
Definition at line 151 of file run_control.h.
| double sander_pmemd_cntrl::scnb |
Divide 1-4 vdW interactions by scnb; GLYCAm needs = 1.0;.
Definition at line 152 of file run_control.h.
| double sander_pmemd_cntrl::taup |
Pressure relaxation time = 0.1;.
Definition at line 154 of file run_control.h.
| double sander_pmemd_cntrl::tautp |
Time constant for heat-bath coupling; default = 1.0;.
Definition at line 155 of file run_control.h.
| double sander_pmemd_cntrl::temp0 |
Desired constant temperature (kelvin)
Definition at line 156 of file run_control.h.
| double sander_pmemd_cntrl::tempi |
Initial temperature.
Definition at line 157 of file run_control.h.
1.7.6.1 
