[gmx-users] About frozen groups
mohkam978 at hotmail.com
Wed Jan 21 03:40:09 CET 2009
Many thanks for Justin for your helpful comments, I think I still need your help for the first question... I have included more details about my system below
> 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
Thanks much for that advice
> > > > > 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.>
IRS is a group of residues in the protein, suppose that my protein has 50 residues, IRS is a group that contains residues 2, 7, 9, 15, 45 for example. So the IRS group is actually part of my protein
Now I have four groups the SOL, ligand (T27), protein and IRS which overlapped with the protein (this is the problem) ...
I need to fix the position of IRS residues and exclude the non-bonding interactions between these residues and the solvent. Gromacs will not accept IRS as an energy group because there will be some residues that are common with the protein and so I can't state it in the energy exclusions??
> > *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>
That's fine... so if I just add unconditional #include "POSRE_IRS.itp" to the .top file Gromacs will apply postion restraints even without adding the define line to the .mdp file?
> -Justin> > > * *> > > > Looking forward for your kind suggestions and comments> > > > > > > > Great Thanks> > > > Mohammed
**************************************************Mohammed K. Abdel-HamidPhD CandidateSchool of Chemistry University of Wollongong Northfields Ave. Wollongong, NSW, 2522
Ph: +61 2 4221 3510Fax: +61 2 4221 4287
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