Hi Justin, I am sorry, I switched the radius and the numbers: radius=0 charge=1 mass=1
But I already tried it without the membrane and there I had the same problem. And also when I did not restrained anything. Not even the membrane I got the high force and the LINCS warnings. Of what physical problems do you think? I already looked at the protein with Pymol and the residue with the high force does not in interact with any other. > > > On 10/18/12 8:51 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi Justin, >> >> Well I already tried the protein without the membrane and I got the same >> result. And I also make sure that I had no error messages during the >> preparation runs. >> > > If the protein crashes in the absence of anything else, then likely you > have > problems with its starting geometry. Applying restraints during > minimization is > probably causing the clashes to be insufficiently resolved. > >> I am using the amber03 force field. >> My dummy atoms have a radius of 1.00 and a charge of 0.00. And yes they >> are non bonded atoms. >> > > Radius of 1.0 nm? If the crash occurs without these atoms, then it's > likely > irrelevant, but with particles 10 times the size of normal atoms, you may > be > asking for trouble. > > -Justin > > >>> On 10/18/12 7:05 AM, reising...@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, reising...@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 >>>>>>> reising...@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-boun...@gromacs.org >>>>>>>>> [mailto:gmx-users-boun...@gromacs.org] >>>>>>>>> Im Auftrag von reising...@rostlab.informatik.tu-muenchen.de >>>>>>>>> Gesendet: Donnerstag, 18. Oktober 2012 10:56 >>>>>>>>> An: gmx-users@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@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-requ...@gromacs.org. >>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>>>> -- >>>>>>>>> gmx-users mailing list gmx-users@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-requ...@gromacs.org. >>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> gmx-users mailing list gmx-users@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-requ...@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 >>>>>>> er...@xray.bmc.uu.se >>>>>>> http://www2.icm.uu.se/molbio/elflab/index.html >>>>>>> >>>>>>> -- >>>>>>> gmx-users mailing list gmx-users@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-requ...@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@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-requ...@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@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-requ...@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@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? 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