[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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