[gmx-users] infinite force at the membrane lipid
Vy Phan
phanvy120690 at gmail.com
Sun Aug 16 14:14:56 CEST 2015
Dear HTH and Gromacs Users,
Thank you HTH,
I used the DOPC membrane lipid pdb file and topology from the website
http://mmkluster.fos.su.se/slipids/Downloads.html.
I running energy minimization for protein in water and lipid in water.
After that, I put the protein into the center of membrane lipid and use tcl
script to remove all overlapping moleculas by this script.
[atomselect 0 " resname DOPC and (same residue as resname DOPC and x >25
and x<110 and y > 20 and y < 115) and not (same residue as resname DOPC and
within 1 of protein)"] writepdb DOPC.pdb
[atomselect 0 " water and (same residue as water and x > 20 and x<115 and y
> 15 and y < 120) and not (same residue as water and within 1 of protein)"]
writepdb wat.pdb
After that I combine protein, lipid and water to one system and run.
I did not use inflate_gro or g_membed tools. The g_membed tools can not
used in Gromacs 5 (I use Gromacs 5.0.4)
Hope you can see my problems and help me more.
If you think the way I insert the protein on the lipid is the problem.
Please let me know. I usually do this way with NAMD.
Best regards,
Tuong Vy
2015-08-16 20:21 GMT+09:00 ABEL Stephane 175950 <Stephane.ABEL at cea.fr>:
> Hello,
>
> How did you construct your membrane, with CHARMM-GUI? What is the lipid?
> From my experience, I have found that sometimes CHARMM-GUI does not provide
> a good starting point for MD. So I would suggest you to :
>
> - center the lipids inside the box to have no lipids that cross the box
> limit and/or increase a little bit the box size (x-y) and minimize your
> system again.
>
> Moreover to insert you protein inside the membrane, did you try the
> inflate_gro or g_membed tools ?
>
> Good luck
>
> HTH
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 16 Aug 2015 10:51:42 +0900
> From: Vy Phan <phanvy120690 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] infinite force at the membrane lipid
> Message-ID:
> <CAC+3Te00hidSrXE49g5mfqvCsBSaE5wTJ-NtFubaXvvz=
> U68+g at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Dr Justin and Gromacs User,
>
> This is my commands for running energy minimization.
>
> define = -DPOSRES
> integrator = cg
>
> nstcgsteep = 1000
> emtol = 100.0
> emstep = 0.01
> dt = 0.002
> ; Output control
> nstxout = 50
> nstenergy = 50
> nstlog = 50
>
>
> nstlist = 1
> cutoff-scheme = Verlet
> ns_type = grid
> coulombtype = PME
> rcoulomb = 1.2
> vdw-modifier = Potential-shift
> rvdw = 1.2
> rvdw-switch = 1.0
> pbc = xyz
>
>
> I hope you can give more recommendations. Removing lipids actually is not
> an appropriate solution.
>
> Thank you so much
>
> Tuong Vy
>
> 2015-08-16 1:47 GMT+09:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > On 8/15/15 12:41 PM, Vy Phan wrote:
> >
> >> Dear All gromacs Users,
> >>
> >> I want to run the membrane protein simulation. I run the energy
> >> minimization for membrane and protein separately.
> >> After that I combine protein and lipid together and remove the
> >> overlapping
> >> molecules.
> >> when I run energy minimization I got the error "inf at atom on lipid". I
> >> remove the lipid which includes this atom. I got the error several time
> >> and I repeat remove lipid. I see the "inf at atom on lipid" always
> happens
> >> on lipids which locate at the wall (at the boundary of unit cell).
> >>
> >> I successfully run one time when I remove lipids have error, another
> was
> >> failed.
> >>
> >> I wonder why the error "inf at atom on lipid" always happens on lipids
> >> which locate at the wall. Maybe I did something wrong about periodic
> >> boundary condition.
> >>
> >> Thank you for any thoughts.
> >>
> >>
> > Without a list of your exact commands and what you've done to this point,
> > it's impossible to diagnose. There's something fundamentally wrong with
> > the coordinates, topology, or both. If the infinite force is just moving
> > around, what you're observing is a symptom, not a cause, and removing
> > lipids to try to make it go away is not an appropriate solution.
> >
> > -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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