This is not an NVT run. This is EM. Furthermore, I don't see the point in combining position restraints with EM.
Erik 18 okt 2012 kl. 12.15 skrev [email protected]: > 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. > > Thank you , > Eva > > >> 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 >> > > > -- > 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
