[gmx-users] Fwd: segmentation fault on gpus
rmbio861 at gmail.com
Tue Jun 24 18:14:59 CEST 2014
Thanks, that makes sense, however I was able to use the same ligand toplogy
files with earlier versions like gromacs 4.5.4 to simulate protein ligand
complexes. I can simulate protein-ligand complexes with the current
versions also but only for the crystal structures that have ligand bound to
it, not the modelled proteins with ligands bound.
and also I would appreciate any comments on the mdp file as below:
title = Bilayer-500
cpp = /lib/cpp
constraint_algorithm = lincs
constraints = all-bonds; added
lincs_iter = 1; added
lincs_order = 4; added
integrator = md;
dt = 0.002
tinit = 0;
nsteps = 1000000 ; 2 ns
nstcomm = 500
nstxout = 5000
nstvout = 5000
nstfout = 0
nstxtcout = 500
xtc_precision = 1000
nstlog = 500
nstenergy = 500
nstlist = 50
ns_type = grid; added
nstcalclr = 1
; long range interactions
coulombtype = PME
rlist = 1.4
rcoulomb = 1.2
rvdw = 1.2
fourierspacing = 0.16
pme_order = 4
vdw-type = Cut-off
cutoff-scheme = Verlet
Tcoupl = v-rescale
tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 0.1
tc-grps = Protein POP SOL NA CL LIG SOD CLA
ref_t = 303 303 303 303 303 303 303 303
; Energy monitoring
energygrps = Protein POP SOL SOD CLA LIG NA CL
Pcoupl = Berendsen
pcoupltype = semiisotropic
tau_p = 1.0 1.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
DispCorr = no ; added
;generate velocites is on at 293K
gen_vel = yes
gen_temp = 303.0
gen_seed = 478905
comm-mode = Linear
comm-grps = System
On Mon, Jun 23, 2014 at 8:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 6/23/14, 5:53 PM, ram bio wrote:
>> Dear Gromacs Users,
>> I have been trying to simulate protein-ligand complex using gromacs
>> versions that use verlet cutoff scheme on gpus.
>> These are some of the issues that i could resolve, and any kind of
>> suggestion or help is appreciated.
>> 1. With gromacs 4.6.5 i could simulate crystal structure from pdb but not
>> modelled protein with ligand always ended up in segmentation fault. The MD
>> run during equillibration runs for gew thousands of steps and errors out
>> segmentation fault, so i have to rerun using previous cpt file, for a run
>> of 2ns to complete i have to rerun it for 7-10 times.
>> So if the the system id not minimized, why would it go into rerun?
>> 2. I though it could be a bug and used 4.6.3 and 5.0 release, with this
>> trial i could equillibrate just modelled protein but not with the
>> protein-ligand complex. The same error occurs as i mentioned above with
>> protein-ligand complex...
>> I am attaching my mdp file and the minimized structure that i am using for
> The list doesn't accept attachments.
> It seems clear to me that your ligand topology is not stable. If the
> protein works, but the protein+ligand doesn't, what's changing? That's the
> likeliest source of your problem.
> 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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