[gmx-users] About frozen groups

[Justin A. Lemkul]

Mohammed Kamal wrote:

> Tcoupl                   = berendsen
> 
> tau_t                    = 0.1 0.1 0.1 0.1
> 
> tc_grps                  = protein T27 SOL Cl ; T27 is the ligand

General advice: do not couple solvent and ions separately.  I believe there is a 
newer version of the tutorial that fixes this information.  See here:

http://wiki.gromacs.org/index.php/thermostats

> 
> ref_t                    = 300 300 300 300
> 
> *energygrps               = protein T27 SOL *
> 
> *energygrp_excl           = IRS IRS IRS SOL*
> 
> *freezegrps               = IRS*
> 
> *freezedim                = Y Y Y*
> 
> Pcoupl                   = berendsen
> 
> pcoupltype               = isotropic
> 
> tau_p                    = 0.5
> 
> compressibility          = 4.5e-5
> 
> ref_p                    = 1.0
> 
> gen_vel                  = yes
> 
> gen_temp                 = 300
> 
> gen_seed                 = 173529
> 
>  
> 
> and when I used the grommp line of
> 
> *grompp* -f md.mdp -c 2zd1_eq.gro -p 2zd1.top -n IRS.ndx -o md.tpr
> 
> I had (as expected) an error massage states that IRS is not an energy 
> group however if I have added IRS as an energy group I had an error that 
> some atoms are in multiple energy Mon. groups.
> 

Well, what is IRS?  Is it a protein, another molecule?  You've got very 
different groups labeled for energy monitoring and energygrp-excl, so something 
needs to be fixed.  Without any clue what exactly you're dealing with, it's hard 
to give any useful information.

> *So, my first question is how to deal with that problem for including my 
> frozen residues that way?*
> 
> * *
> 
> 2*.* The second method I think about is to just position-restrained 
> these residues where I have created an .itp file for the residues need 
> to be fixed (POSRE_IRS.itp) using/ genpr /command. But I don’t know how 
> to consider that in the calculations….
> 
> *Can I just include this file in the toplogy file (#include 
> “POSRE_IRS.itp”) and add the line Define = -DPOSRE_IRS in my .mdp file??*
> 

Look in your protein topology (if you created one with pdb2gmx) to get the 
syntax right, because, as written no, your approach will not work.  If you 
always #include "POSRE_IRS.itp," then position restraints are always applied. 
To make them conditional

#ifdef POSRE_IRS
#include "POSRE_IRS.itp"
#endif

-Justin

> * *
> 
> Looking forward for your kind suggestions and comments
> 
>  
> 
> Great Thanks
> 
> Mohammed
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
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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