[gmx-users] Fwd: segmentation fault on gpus
Justin Lemkul
jalemkul at vt.edu
Wed Jun 25 11:55:25 CEST 2014
On 6/24/14, 2:11 PM, ram bio wrote:
> shall i do only two tc-grps protein and non-protein?
>
Not for a membrane protein system, no. I'd say your complex, the lipids, and
solvent+ions in three groups is the most common approach.
-Justin
>
> On Tue, Jun 24, 2014 at 12:18 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.
>>
>>
>> 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
>>>
>>
>> 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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>> * Please search the archive at http://www.gromacs.org/
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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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