[gmx-users] Increase the box size or decrease rlist
pragnapcu at gmail.com
Wed Aug 20 16:33:55 CEST 2014
I could solve the fatal error by giving box vectors 4.84331 4.84331 6.69130
while generating .gro file from .pdb using editconf.
Then, the following warning:
WARNING 1 [file minim.mdp]:
You are using full electrostatics treatment PME for a system without
This costs a lot of performance for just processing zeros, consider using
So, should i give -maxwarn 1 or change the electrostatics from 'PME' to
'Cut-off'. Can anyone please suggest?
On Wed, Aug 20, 2014 at 8:55 AM, pragna lakshmi <pragnapcu at gmail.com> wrote:
> Thank u Justin for your reply.
> I have realized that stockholm lipids are derived from Amber ff. But i am
> unable to get parameters for POPC derived from charmm ff. Is there any
> source for that?
> The box vectors that are listed in POPC.gro are 0.00000 0.00000
> On Tue, Aug 19, 2014 at 11:50 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 8/19/14, 2:14 PM, pragna lakshmi wrote:
>>> Dear all,
>>> I am trying to do MD simulation of POPC membrane simulation with
>>> attachment of protein ligand complex. Steps that i have performed so far
>>> 1. orienting the protein with editcong -princ command
>>> 2. rotating it along the y-axis with editconf -rotate 0 40 0 command
>>> 3. separation of protein ligand files into individual files and
>>> of topology file of protein from pdb2gmx and ligand from swissparam.
>>> (charmm 36ff was used for protein topology generation. source:
>>> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs )
>>> 4. The protein and ligand files were merged followed by necessary changes
>>> in topology file.
>>> 5. Pre-equilibrated POPC bilayer was downloaded from Dr.Klauda's website
>>> whereas its itp file was taken from Stockholm_Lipids website.
>> The Stockholm lipids are derived from Amber force fields. You can't
>> combine them with CHARMM protein parameters and expect anything physically
>> meaningful. If you're using the CHARMM protein force field, use the CHARMM
>> lipid parameters.
>> 6. After this, when i am running the command
>>> grompp -f minim.mdp -c POPC.gro -p POPC.top -o em_POPC.tpr
>>> i am facing the fatal error:
>>> ERROR: The cut-off length is longer than half the shortest box vector or
>>> longer than the smallest box diagonal element. Increase the box size
>>> decrease rlist.
>> What are the box vectors listed in POPC.gro?
>> As it is suggesting, I have decreased rlist, rcoulomb and rvdw from 1.2
>>> 1.0. But still the same error is raising.
>> Don't mess with these settings just to make an error message go away.
>> The nonbonded setup is a fixed feature of the force field, and lipids are
>> especially sensitive to changes here. I just posted the proper settings
>> for the CHARMM force field a few days ago; use those settings and don't
>> deviate unless you have proof that what you're doing is superior.
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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> Pragna Lakshmi.T,
> Ph.D. Scholar,
> IPLS Project,
> Pondicherry University,
> India - 605014.
India - 605014.
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