[gmx-users] energy minimization problem

Ming Tang m21.tang at qut.edu.au
Mon May 18 11:47:57 CEST 2015 

Besides, the martini.itp does not contain  moleculetype CL, so I edit it like this:

[ moleculetype ]
; molname  	nrexcl
  CL 	    	1

[ atoms ]
;id 	type 	resnr 	residu 	atom 	cgnr 	charge
 1 	P4 	1 	CL 	CL 	1 	    -1

Please help to have a look. I do not know whether it is true or not, as the small triple helix used for test does not carry charge, so I did not add CL.

Thanks.

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Ming Tang
Sent: Monday, 18 May 2015 7:04 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] energy minimization problem




Hi Tsjerk,

I used the original structure generated by sabbac.

My computer has 8 cores only, martini simulation looks much faster than full atomic simulation.

The command I used is here:

python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys -p backbone -ff martini22 -collagen

editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb

grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o minimization-vaccum.tpr mdrun -deffnm minimization-vaccum -v

gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o system-solvated.gro

I downloaded the CG water model from martini protein tutorial website. Is there anything wrong?


-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar
Sent: Monday, 18 May 2015 6:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] energy minimization problem

Hi Ming Tang,

That's pretty quick. I guess that this is on multiple cores, given the size of the system. It often helps to equilibrate on a limited number of cores, but I'm not sure that's feasible.

Did you obtain the model by martinizing the original structure, or did you use the relaxed structure from the atomistic simulation? How did you solvate the system?

Cheers,

Tsjerk
On May 18, 2015 10:29, "Ming Tang" <m21.tang at qut.edu.au> wrote:

> Hi Tsjerk,
>
> I just tried, but it stopped for too many LICS warnings at step 6000.
> Small triple helix can be equilibrated for 1000ns with NPT.
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Tsjerk 
> Wassenaar
> Sent: Monday, 18 May 2015 6:21 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] energy minimization problem
>
> Hi Ming Tang,
>
> Can you run in NVT? Then afterwards you can try NPT without position 
> restraints.
>
> Cheers,
>
> Tsjerk
> On May 18, 2015 10:14, "Ming Tang" <m21.tang at qut.edu.au> wrote:
>
> > Thanks a lot, Justin
> >
> > It really makes me feel weird. The small triple helix with 30 amino 
> > acids per chain(generated simply by deleting other atoms in .pdb 
> > file of the real triple helix) can be equilibrated for 1ns using 
> > exactly the same control files, and the real triple helix can be 
> > used for full atomic simulation without any problem. The CG topology 
> > is generated using the same mitinize.py downloaded from the website.
> > I will try for another time, and will tell you if I fix it.
> >
> > Thanks.
> >
> > -----Original Message-----
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of 
> > Justin Lemkul
> > Sent: Sunday, 17 May 2015 7:07 AM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] energy minimization problem
> >
> >
> >
> > On 5/16/15 8:30 AM, Ming Tang wrote:
> > > Dear Justin,
> > >
> > > I tried to use small time step. First,  set dt=0.005ps, after 
> > > running
> > 20ps, I found one chain of the triple helix just went to another 
> > water box totally. I guess there is something wrong with the martini 
> > ff because of the small time step.
> > > Then, I increased it to 0.01ps, after running 40ps, I checked the 
> > > .gro,
> > and found all the three chains stay together, which is reasonable.
> > However, even use dt=0.01, the simulation can only run about 1ns. 
> > And, after simulating 100 ps using dt=0.01ps, the simulation can 
> > just run thousands of steps when dt is increased to 0.02ps. I tried 
> > many times and many different time steps, but still could not see 
> > the possibility for it to run hundreds of  nanoseconds, which is 
> > quite normal when using martini force. If the system can be further 
> > minimized, then it can
> run longer maybe.
> > >
> >
> > This seems entirely random and suggests instead that there is 
> > something simply physically unstable with the system or problematic 
> > in
> the topology.
> > I don't use MARTINI (or CG models in general) so there's little else 
> > I can suggest.  Maybe someone more experienced with such systems 
> > will
> chime in.
> >
> > Also note that a chain "moving into another box" is probably just a 
> > PBC effect and not a true dissociation.  If it is a dissociation, 
> > it's not simply because of the time step.
> >
> > -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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