[gmx-users] Position Restrain md

Jamie Seyed jamie.seyed at gmail.com
Sat Aug 15 02:52:46 CEST 2009

Hi Mark,
Thanks for the answers. One question still remains for me: in the fws
tutorial for PR step it only uses the pr.mdp (define = -DPOSRES) and run
grompp followed by mdrun... Am I missing some thing? Because I can not see
it introduces something that to be restrained..?? Would you please let me
know what I am missing here?? Many Thanks in Advance/Jamie
On Fri, Aug 14, 2009 at 8:33 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> Jamie Seyed wrote:
>> Dear all,
>> I have questions regarding the position restrain md. I tried to find the
>> answer of my questions from the mailing list, but it is not clear yet.
>> In the fws tutorial when it says (in the pr.mdp)
>> tc_grps=Protein   non-protein
>> (1) Doesn't that mean everything in the system? I think for this case we
>> can
>> simply write "system" because system is made by protein and non-protein??
> It includes the whole system, but it is often a good idea not to couple
> groups of heterogeneous heat capacity to the same thermostat. That said, if
> the groups are too small, you get other problems. See also
> http://oldwiki.gromacs.org/index.php/temperature_coupling
> (2) In this case how program recognize which one should restrain and which
>> one not, because it included all??
> Temperature coupling has no linkage with position restraints. You defined
> the latter in your .top file.
> (3) This step is required for every system or only proteins??
> It may or may not be useful in achieving stable equilibration for any
> system. See
> http://oldwiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
> (4) If I want to make an index file and I specify a group that need to be
>> constrained, in the generated index file I will get system and all its
>> parts
>> and an extra part for my specific part that need to be constrain...Is that
>> ok??
> "constraints" are different from "restraints" in GROMACS usage. make_ndx
> does allow you to generate new index groups, but you will need to (re-)read
> the relevant manual sections to understand that neither of these algorithms
> uses index groups. (Or to prove my memory wrong!)
> (5) In my case I have a molecule (MOL) and water (SOL), for position
>> restrain md should I use "tc_grps=MOL   SOL" (according to fws tutorial)
>> or
>> I need only write "tc_grps=MOL"??  Many Thanks in Advance/Jamie
> The latter won't work, for all atoms must be members of a
> temperature-coupling group if any are.
> What you actually need is a clear understanding of your strategic
> objective. Hopefully some of the links will move you towards that.
> Mark
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