[gmx-users] to know about constraints
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Jun 20 09:37:32 CEST 2012
On 20/06/2012 5:24 PM, Anik Sen wrote:
> 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
Look at the requirements for freeze groups in manual section 7.3...
Mark
>
> Is the .mdp wrong please suggest
>
> ________________________________________
> 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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