[gmx-users] to know about constraints
Anik Sen
aniksen at csmcri.org
Tue Jun 19 20:35:09 CEST 2012
Hello Justin,
This is Anik again.
I checked the links. But could not understand fully. Am giving the part of the topology file as given below, generated with the command
"pdb2gmx -f a.pdb -o b.pdb -p topol.top"
The topology file :
" 205 CL- 205 CL- Cl 205 -1 35.453 ; qtot 35
206 CL- 206 CL- Cl 206 -1 35.453 ; qtot 34
207 CL- 207 CL- Cl 207 -1 35.453 ; qtot 33
208 CL- 208 CL- Cl 208 -1 35.453 ; qtot 32
209 CL- 209 CL- Cl 209 -1 35.453 ; qtot 31
210 CL- 210 CL- Cl 210 -1 35.453 ; qtot 30
211 CL- 211 CL- Cl 211 -1 35.453 ; qtot 29
212 CL- 212 CL- Cl 212 -1 35.453 ; qtot 28
213 CL- 213 CL- Cl 213 -1 35.453 ; qtot 27
214 CL- 214 CL- Cl 214 -1 35.453 ; qtot 26
215 CL- 215 CL- Cl 215 -1 35.453 ; qtot 25
216 CL- 216 CL- Cl 216 -1 35.453 ; qtot 24
217 CL- 217 CL- Cl 217 -1 35.453 ; qtot 23
218 CL- 218 CL- Cl 218 -1 35.453 ; qtot 22
219 CL- 219 CL- Cl 219 -1 35.453 ; qtot 21
220 CL- 220 CL- Cl 220 -1 35.453 ; qtot 20
221 CL- 221 CL- Cl 221 -1 35.453 ; qtot 19
222 CL- 222 CL- Cl 222 -1 35.453 ; qtot 18
223 CL- 223 CL- Cl 223 -1 35.453 ; qtot 17
224 CL- 224 CL- Cl 224 -1 35.453 ; qtot 16
225 CL- 225 CL- Cl 225 -1 35.453 ; qtot 15
226 CL- 226 CL- Cl 226 -1 35.453 ; qtot 14
227 CL- 227 CL- Cl 227 -1 35.453 ; qtot 13
228 CL- 228 CL- Cl 228 -1 35.453 ; qtot 12
229 CL- 229 CL- Cl 229 -1 35.453 ; qtot 11
230 CL- 230 CL- Cl 230 -1 35.453 ; qtot 10
231 CL- 231 CL- Cl 231 -1 35.453 ; qtot 9
232 CL- 232 CL- Cl 232 -1 35.453 ; qtot 8
233 CL- 233 CL- Cl 233 -1 35.453 ; qtot 7
234 CL- 234 CL- Cl 234 -1 35.453 ; qtot 6
235 CL- 235 CL- Cl 235 -1 35.453 ; qtot 5
236 CL- 236 CL- Cl 236 -1 35.453 ; qtot 4
237 CL- 237 CL- Cl 237 -1 35.453 ; qtot 3
238 CL- 238 CL- Cl 238 -1 35.453 ; qtot 2
239 CL- 239 CL- Cl 239 -1 35.453 ; qtot 1
240 CL- 240 CL- Cl 240 -1 35.453 ; qtot 0
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "tip4p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif "
This includes the posre.itp as follows:
" ; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.
[ position_restraints ]
; atom type fx fy fz
215 1 1000 1000 1000
216 1 1000 1000 1000
217 1 1000 1000 1000
218 1 1000 1000 1000
219 1 1000 1000 1000
220 1 1000 1000 1000
221 1 1000 1000 1000
222 1 1000 1000 1000
223 1 1000 1000 1000
224 1 1000 1000 1000
225 1 1000 1000 1000
226 1 1000 1000 1000
227 1 1000 1000 1000
228 1 1000 1000 1000
229 1 1000 1000 1000
230 1 1000 1000 1000
231 1 1000 1000 1000
232 1 1000 1000 1000
233 1 1000 1000 1000
234 1 1000 1000 1000
235 1 1000 1000 1000
236 1 1000 1000 1000
237 1 1000 1000 1000
238 1 1000 1000 1000
239 1 1000 1000 1000
240 1 1000 1000 1000 "
Now are these atoms already restrained, or we have to restrain tem by othr means..
As after the minimisation step, the atoms are moving from their positions, which i donot want.
Please help in this matter.
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Anik Sen [aniksen at csmcri.org]
Sent: Tuesday, June 19, 2012 11:13 PM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: RE: [gmx-users] to know about constraints
Thanx Justin.
I will check the links..
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Tuesday, June 19, 2012 11:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] to know about constraints
On 6/19/12 1:28 PM, Anik Sen wrote:
> Dear gromacs developers,
>
> This is Anik. For a certain work with
> nonbonded interactions with alkali halides and water, I need to constrain some
> specific atoms in the energy minimization step. Is there any option to constrain
> the atoms in a specific calculation. The water molecules and other atoms may be
> in movement during the calculation.
>
I think what you're looking for are "restraints," not "constraints." Restraints
inhibit motion; constraints fix bond lengths or angles.
http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
Position restraints are a common part of many workflows. These are likely what
you need.
http://www.gromacs.org/Documentation/How-tos/Position_Restraints
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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