[gmx-users] distance restraint in gromacs md run

[Simon Kit Sang Chu]

Hi Mark,

I thought including distance restraint file here would still be valid?
Although this is called POSRES, the file included in not position restraint
but distance restraint.


; Include distance restraint file
#ifdef POSRES
#include "p1p2_dist.itp"
#endif


I try to simulate a trial system and the two chains which are supposed to
be distance restrained, eventually disassemble. I first
thought DISPRES could be replaced by POSRES, i.e. the naming is arbitrary.
It does not seem to be the case.

Right now, I choose "define  = -DDISRES" and "disre = simple". However, the
message returned indicated that distance restraint is not available in MPI.
Is that so?

Simon

2017-06-19 19:48 GMT+08:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 6/19/17 1:51 AM, Simon Kit Sang Chu wrote:
>
>> Hi,
>>
>> I have a protein of interest which requires distance restraint for C alpha
>> atoms. However, the simulation does not seem to include the restraint at
>> all.
>>
>> *prod.mdp*
>> define              = -DPOSRES
>> constraints         =  none
>> integrator          =  md
>> dt                  =  0.005
>> nsteps              =  40000000         ; 200 ns
>>
>>
>>
>> *p1p2-merged.top*
>>
>> ; Include forcefield parameters
>> #include "ffPACE_1.3.itp"
>>
>> [ moleculetype ]
>> ; Name            nrexcl
>> Protein_A         3
>>
>> [ atoms ]
>> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
>>     chargeB      massB
>>       1         N+      1    MET      N      1        0.7         17   ;
>> qtot 0.7
>> .
>> .
>> .
>>   1861  1862  1863  1864     1
>>
>> ; Include distance restraint file
>> #ifdef POSRES
>> #include "p1p2_dist.itp"
>> #endif
>>
>> *p1p2_dist.itp*
>> ; distance restraints for r_1-62_r_115-176_&_C-alpha of FullP1P2 in water
>>
>> [ distance_restraints ]
>> ;   i     j ? label      funct         lo        up1        up2     weight
>>      2    11 1     0          1   0.283898   0.483898     1.4839
>> 1
>>      2    17 1     1          1   0.552993   0.752993    1.75299
>> 1
>> .
>> .
>> .
>>
>>   Do I need to use "define = -DDISTRES" and "ifdef DISPOSRES" instead?
>>
>
> No, because you haven't enclosed your [distance_restraints] in any #ifdef
> block, so they are always active.
>
> Is
>
>> distance restraint only used in NMR refinement but not MD?
>>
>>
> No, they can be used during any process.  There are relevant .mdp options
> that must be set, though (see the manual).
>
> How have you determined that the restraints aren't working?
>
> -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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