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 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 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 > -- 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
