AW: [gmx-users] question about the minimization
Justin Lemkul
jalemkul at vt.edu
Thu Oct 18 13:45:50 CEST 2012
On 10/18/12 7:05 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi Justin,
>
> I already read the page you send me.
> And I am sure about the first points. But I am not completely sure about
Sure about the first five points? The five suggestions on the page I linked are
all diagnostic steps. What did they turn up?
> the mdp file for the nvt run.
>
> It looks like this:
>
> define = -DPOSRES
> integrator = md
> dt = 0.002
> nsteps = 10000
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstlog = 1000
> nstxtcout = 0
> nstenergy = 5
> energygrps = Protein Non-Protein
> nstcalcenergy = 5
> nstlist = 10
> ns-type = Grid
> pbc = xyz
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 0.9
> rvdw = 0.9
> fourierspacing = 0.12
> pme_order = 4
> ewald_rtol = 1e-5
> gen_vel = yes
> gen_temp = 200.0
> gen_seed = 9999
> constraints = all-bonds
> tcoupl = V-rescale
> tc-grps = Protein Non-Protein
> tau_t = 0.1 0.1
> ref_t = 298 298
> pcoupl = no
>
What force field are you using? What about my questions related to your
so-called dummy atoms? What are they and what are their parameters? Your
minimization seemed fine, so there's clearly something wrong with the physical
model that leads to a crash during MD. At present, there's not enough
information to say exactly what.
-Justin
>
> Thank you for your help,
> Eva
>
>
>>
>>
>> On 10/18/12 6:15 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>>> Hi Erik,
>>>
>>> my .mdp file looks like this:
>>>
>>> define = -DPOSRES
>>> integrator = steep
>>> emtol = 10
>>> nsteps = 30000
>>> nstenergy = 1
>>> energygrps = System
>>> coulombtype = PME
>>> rcoulomb = 0.9
>>> rvdw = 0.9
>>> rlist = 0.9
>>> fourierspacing = 0.12
>>> pme_order = 4
>>> ewald_rtol = 1e-5
>>> pbc = xyz
>>>
>>>
>>> And yes, I use constraints. I have a membrane represented by dummy atoms
>>> around my protein. They are fixed and I also fixed the backbone. Or is
>>> that a problem.
>>>
>>
>> The EM seems to have worked fine, so we need the .mdp file for NVT, not
>> EM.
>> Your membrane representation could be an issue, but I'm not clear on the
>> terminology here. A "dummy atom" (or virtual site) is a particle with
>> nonbonded
>> parameters but no mass. Is that what you're dealing with? If this
>> membrane
>> environment is fixed and the backbone is too, you may get clashes in the
>> system,
>> but it doesn't sound like there's a whole lot that's moving in the first
>> place.
>> General troubleshooting advice (that I seem to post almost daily):
>>
>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>>
>> Your simulation is failing fairly early, so finding the source of the
>> crash
>> should not be terribly difficult.
>>
>> -Justin
>>
>>
>>>> It could be due to your mdp-settings. What's your time step? Do you use
>>>> constraints and virtual interaction sites?
>>>>
>>>> Erik
>>>>
>>>> 18 okt 2012 kl. 12.04 skrev
>>>> reisingere at rostlab.informatik.tu-muenchen.de:
>>>>
>>>>> Hi Felix,
>>>>> thank you for your answer.
>>>>> So you think that a force of 3.2341940e+02 is okey? To work on?
>>>>>
>>>>> I also tried to work on with a NVT run but then I got many many LINCS
>>>>> warnings:
>>>>>
>>>>> Step 1114, time 2.228 (ps) LINCS WARNING
>>>>> relative constraint deviation after LINCS:
>>>>> rms 0.000169, max 0.001796 (between atoms 3480 and 3482)
>>>>> bonds that rotated more than 30 degrees:
>>>>> atom 1 atom 2 angle previous, current, constraint length
>>>>> 3480 3482 30.3 0.1090 0.1092 0.1090
>>>>>
>>>>> Step 1121, time 2.242 (ps) LINCS WARNING
>>>>> relative constraint deviation after LINCS:
>>>>> rms 0.000108, max 0.000561 (between atoms 2000 and 2001)
>>>>> bonds that rotated more than 30 degrees:
>>>>> atom 1 atom 2 angle previous, current, constraint length
>>>>> 2002 2005 30.4 0.1090 0.1090 0.1090
>>>>>
>>>>>
>>>>>
>>>>> And in the end there is the error:
>>>>>
>>>>> Fatal error:
>>>>> 11 particles communicated to PME node 2 are more than 2/3 times the
>>>>> cut-off out of the domain decomposit
>>>>> ion cell of their charge group in dimension x.
>>>>>
>>>>>
>>>>> I looked it up on the GROMACS site and it was written there that such
>>>>> a
>>>>> error is caused by a not well equilibrated system.
>>>>>
>>>>> So I thought that the high force might be the reason.
>>>>>
>>>>> What do you think?
>>>>>
>>>>> Thanks again!!
>>>>>
>>>>>
>>>>>> Hi Eva,
>>>>>>
>>>>>> The change in energy in every step became smaller than the machine
>>>>>> precision can represent (as is stated in the output). In other words:
>>>>>> your
>>>>>> system is minimized to a very high degree.
>>>>>> A value of 10 for the Fmax is very low for a system like yours, even
>>>>>> with
>>>>>> a pure protein in water system you probably wouldn't hit this value.
>>>>>> Furthermore, 30.000 steps for a minimization seems pretty high to me.
>>>>>>
>>>>>> Cheers,
>>>>>> Felix
>>>>>>
>>>>>> -----Ursprüngliche Nachricht-----
>>>>>> Von: gmx-users-bounces at gromacs.org
>>>>>> [mailto:gmx-users-bounces at gromacs.org]
>>>>>> Im Auftrag von reisingere at rostlab.informatik.tu-muenchen.de
>>>>>> Gesendet: Donnerstag, 18. Oktober 2012 10:56
>>>>>> An: gmx-users at gromacs.org
>>>>>> Betreff: [gmx-users] question about the minimization
>>>>>>
>>>>>> Hi everybody,
>>>>>>
>>>>>> I have a question about the minimization of my protein. For this
>>>>>> minimization I fixed the backbone and the membrane atoms which around
>>>>>> my
>>>>>> protein.
>>>>>>
>>>>>> I minimized it 30000 steps long but after step 20385 it stops with
>>>>>> the
>>>>>> output:
>>>>>>
>>>>>> Steepest Descents converged to machine precision in 20385 steps, but
>>>>>> did
>>>>>> not reach the requested Fmax < 10.
>>>>>> Potential Energy = -8.8805600e+05
>>>>>> Maximum force = 3.2341940e+02 on atom 3050
>>>>>> Norm of force = 2.0930219e+00
>>>>>>
>>>>>> I do not see why it can not reach a lower force.
>>>>>>
>>>>>> I already looked at the structure with Pymol and there I saw that the
>>>>>> atom
>>>>>> 3050 is in a loop and do not interact with any other residue.
>>>>>>
>>>>>> My .mdp file looks like this:
>>>>>>
>>>>>> define = -DPOSRES
>>>>>> integrator = steep
>>>>>> emtol = 10
>>>>>> nsteps = 30000
>>>>>> nstenergy = 1
>>>>>> energygrps = System
>>>>>> coulombtype = PME
>>>>>> rcoulomb = 0.9
>>>>>> rvdw = 0.9
>>>>>> rlist = 0.9
>>>>>> fourierspacing = 0.12
>>>>>> pme_order = 4
>>>>>> ewald_rtol = 1e-5
>>>>>> pbc = xyz
>>>>>>
>>>>>> Do you see a reason why it can not reach a force lower than 10?
>>>>>>
>>>>>> Thank you,
>>>>>> Eva
>>>>>>
>>>>>> --
>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>>> * Please don't post (un)subscribe requests to the list. Use the www
>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>> --
>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> -----------------------------------------------
>>>> Erik Marklund, PhD
>>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
>>>> phone: +46 18 471 6688 fax: +46 18 511 755
>>>> erikm at xray.bmc.uu.se
>>>> http://www2.icm.uu.se/molbio/elflab/index.html
>>>>
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> * Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>
>>>
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list