[gmx-users] PR for CG lipid and CG protein

[Justin A. Lemkul]

On 1/9/10 11:25 AM, chris.neale at utoronto.ca wrote:
> Hi Justin,
>
> I just double checked and certainly the confout.gro from my EM run in
> parallel with domain decomposition in mdrun is broken over periodic
> boundaries.
>
> I'm running gromacs-4.0.5 on a nehalem under openmpi. Here is my .mdp file
>

That's really weird.  None of my 4.0.x runs have had that problem.  Now, I am no 
C expert, but I found the following in md.c (taken from the 4.0.5 source):

fprintf(stderr,"\nWriting final coordinates.\n");
if (ir->ePBC != epbcNONE && !ir->bPeriodicMols && DOMAINDECOMP(cr)) {
/* Make molecules whole only for confout writing */
do_pbc_mtop(fplog,ir->ePBC,state->box,top_global,state_global->x);

...after which confout.gro is written.

There are no such lines in the 4.0 source, so I think this was added over the 
course of later development.

I don't know what's going on with your system(s); maybe we should continue any 
other discussion in a new thread, so we don't hijack this one :)  There are also 
several entries in the list archive where users have spotted broken frames in 
the trajectory, but an intact confout.gro.

-Justin

> gpc-f101n084-$ cat em_pos.mdp
> define=-DPOSRES_INDO
> constraints = none
> integrator = steep
> tinit = 0
> nsteps = 5000
> nstcomm = 1
> nstxout = 5000
> nstvout = 5000
> nstfout = 5000
> nstxtcout = 5000
> nstenergy = 5000
> ns_type = grid
> rlist = 1
> rcoulomb = 1
> rvdw = 1
> coulombtype = PME
> ewald-rtol = 1e-5
> optimize_fft = yes
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> gen_seed = -1
>
> ; COM PULLING
> pull = umbrella
> pull_geometry = position
> pull_dim = N N Y
> pull_start = no
> pull_nstxout = 500
> pull_nstfout = 500
> pull_ngroups = 1
> pull_group0 = POPC
> pull_pbcatom0 = 0
> pull_group1 = Protein
> pull_pbcatom1 = 0
> pull_init1 = 0 0 0.0
> pull_rate1 = 0
> pull_k1 = 500.0
> pull_vec1 = 0 0 0
>
>
> Chris.
>
> -- original message --
>
> On 1/9/10 10:49 AM, chris.neale at utoronto.ca wrote:
>> Dear Sunny,
>>
>> I replied a while ago, but it seems to have not made it to the list.
>> When using inflategro with gromacs3, you can run cycles like this:
>>
>> 1. inflategro.pl
>> 2. mdrun (EM)
>> 3. goto 1
>>
>> When running with gromacs4, however, you must run cycles like this:
>>
>> 1. inflategro.pl
>> 2. mdrun (EM)
>> 3. trjconv -pbc mol
>> 4. goto 1
>>
>> since mdrun now writes broken molecules.
>
> Are you sure that recent Gromacs versions still do this? I requested a
> fix (for
> final output configurations only) with the original version 4.0, which I
> thought
> (if memory serves) was fixed as of version 4.0.2, released over a year
> ago. Is
> this not the case? I get intact output structures from everything I've done
> since 4.0.2.
>
> Trajectories certainly still contain "broken" frames, the confout.gro
> should not
> be an issue.
>
> -Justin
>
>>
>> The developer of inflategro.pl, Christian Kandt, is aware of this and
>> may have modified the script to allow broken molecules in inflategro,
>> but if you have a version that is more than 2 months old then it
>> certainly can not handle molecules that are broken over PBC, as lipids
>> usually are near the boundary.
>>
>> Chris.
>

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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