[gmx-users] Fwd: segmentation fault on gpus

[ram bio]

hi Justin,

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
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

Thanks,
Pramod




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
>> as
>> 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
>> equillibration.
>>
>>
> 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
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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