I have a cap "ACE" in the beginning of the protein but this was also defined in the aminoacids.rtp file in the amber03 forcefield
> If you got the same problems with the protein only (and without any > restraints), I wonder if you have any non-standard residues (i.e. ligands > or protein modifications) present in your system? > Because a normal protein should work just fine with the parameters you > gave us. > > -----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 15:28 > An: Discussion list for GROMACS users > Betreff: Re: AW: [gmx-users] question about the minimization > > 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#Diagno >>>>>> sing_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? 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
