[gmx-users] energy minimization problem

[Tsjerk Wassenaar]

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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