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

[Victor Ma]

On Wed, Jun 17, 2015 at 3:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
>

Thank you for the quick response, Justin. This was my mistake. In PROA.itp,
I had the right input, which is
#ifdef REST_ON
#include "PROA_rest.itp"
#endif

I am using the exact set up generated from CHARMM-GUI. But I don't think
that constraints are on. I visualized the simulation. The protein is
wiggling from the very beginning of the equilibration
(step6.1_equilibration).
Anything I can check from the output to make sure that the constraints are
on? Sorry about the question. I am not that familiar with Gromacs.

Thank you!

Victor



>
> #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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