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.
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. Best, Eva > > > On 10/18/12 7:05 AM, [email protected] 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, [email protected] >>> 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 >>>>> [email protected]: >>>>> >>>>>> 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: [email protected] >>>>>>> [mailto:[email protected]] >>>>>>> Im Auftrag von [email protected] >>>>>>> Gesendet: Donnerstag, 18. Oktober 2012 10:56 >>>>>>> An: [email protected] >>>>>>> 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 [email protected] >>>>>>> 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 [email protected]. >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>> -- >>>>>>> gmx-users mailing list [email protected] >>>>>>> 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 [email protected]. >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> gmx-users mailing list [email protected] >>>>>> 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 [email protected]. >>>>>> * 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 >>>>> [email protected] >>>>> http://www2.icm.uu.se/molbio/elflab/index.html >>>>> >>>>> -- >>>>> gmx-users mailing list [email protected] >>>>> 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 [email protected]. >>>>> * 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 [email protected] >>> 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 [email protected]. >>> * 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 [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
