[gmx-users] to know about constraints
Marzinek, Jan
j.marzinek10 at imperial.ac.uk
Wed Jun 20 09:35:01 CEST 2012
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Anik Sen [aniksen at csmcri.org]
Sent: Wednesday, June 20, 2012 8:24 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: RE: [gmx-users] to know about constraints
Hello Justin
For freezefprs, am using the .mdp file as follows:
; title = NACL6
cpp = /usr/bin/cpp
define = -DPOSRE
constraints = none
integrator = steep
freezegrps = K+ CL-
freezedim = N N
.................................................
................................................
The error file is coming as:
Fatal error:
Invalid Freezing input: 2 groups and 2 freeze values
Is the .mdp wrong please suggest
Specify index file which include those two groups (K+ C-) with those names. You should also specify the third dimension for each group I guess:
freezedim = N N Y N N Y
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Wednesday, June 20, 2012 12:09 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] to know about constraints
On 6/19/12 2:35 PM, Anik Sen wrote:
> 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..
Provided that all of those atoms are in the same [moleculetype] in the topology,
this is a correct approach.
> As after the minimisation step, the atoms are moving from their positions, which i donot want.
>
Did you set the correct "define" statement in the .mdp file?
Also note that a position restraint does not completely prevent motion, it just
disfavors it. The magnitude of the energy penalty for displacement depends on
the force constant set in posre.itp. You can also use freezegrps to completely
immobilize any subset of atoms in the system.
-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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