[gmx-users] energy minimization problem

[Ming Tang]

Hi Tsjerk,

This protein has a total charge of 35e, and I added 35 CL to balance the system. Is there any difference between adding CL and not adding CL?
Thank you.

-----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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