Dear Justin, I would like to say that now all things work...but it isn't! I tried to minimize my system with emtol 500 and emstep 0.1, then 0.5, then with emtol 1000 and emstep 0.5 and 1, but this time I did not arrive to convergence. It seems to me that every time I use this system, it "behaves" differently from the previous ones! I'm really sure to make the steps in the same way, since I simply scroll the commands with the arrows and re-submit them! This time, I didn't noticed a difference in the number of water molecules after genbox: I re-tried a couple of times the entire procedure, but all was going wrong in the same way... Despite this, I tried to send a PR-MD with the suggested correction on PME (I simply added "coulombtype = PME" in the pr.mdp file) and this is the error message I found (at least, it is different from previous ones...):
Step 502, time 1.004 (ps) LINCS WARNING relative constraint deviation after LINCS: max 25670116.000000 (between atoms 1615 and 1616) rms 674225.375000 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 168 169 89.9 0.1000 0.1254 0.1000 171 172 37.0 0.1000 0.1013 0.1000 171 173 89.9 0.1000 0.1157 0.1000 174 175 89.9 0.1000 0.1299 0.1000 174 176 60.8 0.1000 0.0995 0.1000 1564 1565 34.6 0.1000 0.1001 0.1000 1592 1594 39.6 0.1330 0.1831 0.1330 1594 1595 43.8 0.1000 0.1448 0.1000 1594 1596 111.2 0.1470 3329.0908 0.1470 1596 1597 105.8 0.1530 3329.1094 0.1530 1596 1603 105.5 0.1530 21318.4980 0.1530 1597 1598 36.5 0.1530 0.1972 0.1530 1600 1602 89.8 0.1000 0.2606 0.1000 1603 1604 105.8 0.1230 21076.9980 0.1230 1603 1605 102.2 0.1330 95833.0078 0.1330 1605 1606 100.2 0.1000 87086.0078 0.1000 1605 1607 93.6 0.1470 464589.8125 0.1470 1607 1608 93.4 0.1530 464721.6250 0.1530 1607 1615 95.8 0.1531 768441.6250 0.1530 1608 1609 96.3 0.1530 109266.5625 0.1530 1609 1610 96.6 0.1530 16824.1641 0.1530 1610 1611 120.4 0.1230 2709.7004 0.1230 1610 1612 114.4 0.1330 2709.6948 0.1330 1612 1613 53.7 0.1000 0.1715 0.1000 1612 1614 50.3 0.1000 0.1618 0.1000 1615 1616 90.9 0.1250 3208764.5000 0.1250 1615 1617 94.9 0.1250 802098.3125 0.1250 Back Off! I just backed up step501.pdb to ./#step501.pdb.1# Wrote pdb files with previous and current coordinates [lilligrid:22985] *** Process received signal *** [lilligrid:22985] Signal: Segmentation fault (11) [lilligrid:22985] Signal code: Address not mapped (1) [lilligrid:22985] Failing at address: 0x14b50070 [lilligrid:22985] [ 0] /lib64/libpthread.so.0 [0x381440de70] [lilligrid:22985] [ 1] mdrun [0x56cd54] [lilligrid:22985] *** End of error message *** When I repeated the procedure, the errors were not on the same atoms. However, these deviations are on atoms belonging to protein. On the contrary, on the .log files concerning minimization there are errors again on water molecules. Anna -----Messaggio originale----- Da: Justin A. Lemkul [mailto:[email protected]] Inviato: martedì 17 febbraio 2009 16.33 A: Anna Marabotti; Gromacs Users' List Oggetto: Re: help with neighborsearching error Anna Marabotti wrote: > Dear Justin, > I hope you wouldn't mind if I contact you directly, but I think I cannot send > you the requested .log file via > the gmx-users list because the message would be filtered. It is best to keep the discussion on the list; posting short .mdp files (pasted into the text of the mail, not sent as attachments) will not cause your messages to be filtered. > I'm attaching here the em.mdp file and the pr.mdp file I used for my > simulations. For em.mdp, this is the > "last" version, but I made changes on nsteps and emsteps as I described you > previously. I also changed the > emtol raising it down until 500: nothing worked. The only thing I never > changed is the integrator. I never > changed the parameters for PR-MD during all my attempts on this protein. On > other proteins similar to this > one, the file pr.mdp seems to work well. > An emtol of 500 is reasonable (just checking). > About genbox problem, I noticed that a couple of times the number of water > molecules changed even if the box > shape was the same as previously (BTW, the distance I reported is the one > between solute and box edge (i.e., > editconf -d). However, things don't work even when the number of water > molecules is the same. > I still don't understand why this would be happening, but it is probably not your problem (see below). > I forgot to tell that the protein I'm using is a monomeric protein that I > obtained deleting a chain from the > PDB file, in which it appears as a dimer in the crystallographic cell (a > procedure that I applied several > other times without problems). The monomers are not in contact in the PDB > file. I tested both monomers, and > both of them experiment errors. > > Lastly, the GROMACS I'm using is installed in single precision, so I cannot > use the double precision for > minimization. > > I'm almost certain that the problem is a stupid thing that I cannot see, but > it's almost a week that I'm > checking this system and now I'm exhausted! I hope the Murphy's law on errors > will work this time. Please > forgive me! From your pr.mdp file: title = position-restrained dynamics cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 10000 ; total 20 ps. nstcomm = 1 nstxout = 500 nstvout = 500 nstfout = 500 nstlog = 500 nstenergy = 500 nstlist = 500 ns_type = grid rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-Protein ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 300.0 gen_seed = 173529 You have not specified coulombtype, therefore you are using the default of "cut-off." You are probably going to see artefacts of such a setup, which may lead to incorrect behavior; use PME. -Justin > Many many thanks and best regards > Anna > ______________________________________________ > Anna Marabotti, Ph.D. > Laboratory of Bioinformatics and Computational Biology > Institute of Food Science, CNR > Via Roma 64 > 83100 Avellino (Italy) > Phone: +39 0825 299651 > Fax: +39 0825 781585 > Skype: annam1972 > E-mail: [email protected] > Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm > ____________________________________________________ > "If you think you are too small to make a difference, try sleeping with a > mosquito" -- ======================================== Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
