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

[Justin Lemkul]

On 6/17/15 7:06 PM, Victor Ma wrote:
> 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.
>

"Restraints" and "constraints" are different.

http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints

Your protein will wiggle around; the restraints are merely a bias against large 
movements.  There will be a position restraint energy term written to the .log 
and .edr when restraints are active.

-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

==================================================