[gmx-users] how to turn on constraints in CHARMM-GUI generated Gromacs setup?

[Justin Lemkul]

On 6/17/15 6:33 PM, Victor Ma wrote:
> hello Gromacs users:
>
> I am using the CHARMM-GUI to generate a membrane-protein system for me
> which is really convenience. But I am not sure that if the constraints are
> on in my simulation. I am using the default .mdp files generated from
> CHARMM-GUI interface.
> So the .mdp file says,
> define                  = -DREST_ON -DSTEP6_0
>
> And at the bottom of the PROA.itp and POPC.itp, they say,
> #ifdef DREST_ON
> #include "PROA_rest.itp"
> #endif
>
> And both PROA_rest.itp and POPC_rest.itp are present in the work directory.
> It all looks fine. But when I check the output files, such as md.out and
> *.log files, I don't see anything on the constraints. So I suspect that
> it's off. How do I turn it on?

Use the right syntax :)  The -D is a preprocessor prefix.

#ifdef REST_ON
#include "PROA_rest.itp"
#endif

The appropriate #ifdef blocks should already be written to the topology; you 
shouldn't have to modify anything.  The CHARMM-GUI output should work exactly 
as-is out of the box.

>
> Another question is that is it ok to just run the system starting from
> 303K, which is the default setup out of ChARMM-GUI? I thought for
> membrane-protein system, we are supposed to first slowly heat up the system
> from 0 K to the target temperature.
>

That's often unnecessary.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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