[gmx-users] Fwd: segmentation fault on gpus
Szilárd Páll
pall.szilard at gmail.com
Tue Jun 24 19:42:38 CEST 2014
On Tue, Jun 24, 2014 at 7:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 6/24/14, 12:14 PM, ram bio wrote:
>>
>> 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.
>>
>
> So the same ligand works elsewhere, but not in a specific complex? That
> implicates the starting structure or the quality of the protein structure.
> Other notes below.
>
>
>> 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
>
>
> This may work well in terms of GPU performance, but could be problematic if
> there are very sensitive cases.
Why would it be problematic?
>
>> ns_type = grid; added
>> nstcalclr = 1
>> ; long range interactions
>> coulombtype = PME
>> rlist = 1.4
>> rcoulomb = 1.2
>> rvdw = 1.2
Setting rlist != rc doesn't make sense for the Verlet scheme.
>> 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
>
>
> This tc-grp setup is total nonsense.
>
> http://www.gromacs.org/Documentation/Terminology/Thermostats
>
> -Justin
>
>
>> ; 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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>
> --
> ==================================================
>
> 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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> Gromacs Users mailing list
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