Re: [gmx-users] trjconv problem
Hi, thanks for the tips. First I used the information of the exact time I got from g_cluster which did not work (t=5590.093). So I used trjconv to convert the whole trajectory in a pdb-file from which I got the exact time (t=5590.00049) of the frame to be extracted that was different compared to that in g_cluster. By using that as input for trjconv I finally could extract the frame. The -dump option did not work without specifying the exact frame time. Best regards, Björn It might be a rouding problem, so if you want to extract the single frame at time 5590, you might want to try trjconv -b 5589.9 -e 5590.1 -o frame.pdb ... If it still doesn't work: In gromacs 3.3 there was a bug that caused trjconv not to find frames. As far as I know the bug was fixed in Version 3.3.1. cheers, jochen hi, similar happened to me, when i used the -b and -e flags of trjconv. to me it seemed that if you do not hit exactly the time frame as written in the trr file, trjconv will not output anything. when i used the -dump flag it worked, because then frames near the specified time are dumped. hope that helps. marc -- Bjoern Windshuegel Department of Pharmaceutical Chemistry University of Kuopio Harjulantie 1 70211 Kuopio, FINLAND Phone: (+358) 17 162463 Fax: (+358) 17 162456 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] pdb2gmx and ignh
Hi Frisco, Are you by chance using a _united_ atom force field (GROMOS?). And are you wondering where all you're non-polar hydrogens are? Please read the manual (better) and read the papers about the force field you're using. -ignh strips all hydrogens, which is handy if there are hydrogens present which shouldn't be there according to the description in the force field. In that case, all hydrogens which should be there, according to the force field, are added bakc according to a set of geometrical rules. I hope this answers your question. Cheers, Tsjerk On 8/4/06, Frisco Rose [EMAIL PROTECTED] wrote: Hello all, I am confused about what the -ignh option of pdb2gmx actually does. I have read the mailing list, the manual and many tutorials and short of browsing the source cannot find a definite answer. The man page claims that pdb2gmx will add hydrogens, however after using the ignh option to ignore inappropriately named hydrogens in the input pdb (1xq8.pdb) there are many missing hydrogens (nearly a thousand - as far as I can tell) in the output files. Running any calculation with that many missing hydrogens seems very non-physical. It seems that pdb2gmx doesn't like the naming conventions or number of hydrogens in the pdb file. Can someone please explain what -ignh actually does and what the proper method of converting a pdb file from RCSB for use with GROMACS should be? I have tried building the protein from scratch with pymol but pdb2gmx doesn't like pymol generated pdb files either. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] output energies by group
Mu Yuguang (Dr) wrote: Dear all, How to output energies of different groups during the MD simulation? with g_energy, if you have used energy groups in the simulation... No, I mean output the group energies in the flying ( using cut-off, during the simulation, not after the simulation), I think I have to modify the source code. What do you mean in the flying? Best regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
RE: [gmx-users] output energies by group
HI David, in the flying I means I want to output the total potential energy only for protein part ( total system is protein + solvent) when simulating is going on. I want to use that energy for some purpose. I know when using PME is not easy to get the energy group-decomposition, But when I use cut-off, there should be a way to do that, is it? Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, August 05, 2006 3:40 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] output energies by group Mu Yuguang (Dr) wrote: Dear all, How to output energies of different groups during the MD simulation? with g_energy, if you have used energy groups in the simulation... No, I mean output the group energies in the flying ( using cut-off, during the simulation, not after the simulation), I think I have to modify the source code. What do you mean in the flying? Best regards Yuguang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
Re: [gmx-users] output energies by group
David van der Spoel wrote: Mu Yuguang (Dr) wrote: Dear all, How to output energies of different groups during the MD simulation? with g_energy, if you have used energy groups in the simulation... No, I mean output the group energies in the flying ( using cut-off, during the simulation, not after the simulation), I think I have to modify the source code. What do you mean in the flying? Sounds like a double language issue :-) on the fly is an English slang expression for describing doing something while actively engaged in something else... here getting the group energies while still simulating. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
[gmx-users] what is MPI process rank 0 (n0, p18041) caught a SIGSEGV ?
In God We TrustHello GMX users I want to do QM/MM by Gromacs and mopac7.I install Gromacsand mopac7.when I run mdrun it says: Back Off! I just backed up a.log to ./#a.log.5#Reading file a4.tpr, VERSION 3.3 (single precision)QM/MM calculation requested.Layer 0 nr of QM atoms 147QMlevel: PM3/STO-3G MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED MAXIMUM ALLOWED = 200keywords are: PRECISE GEO-OK CHARGE=0 GRAD MMOK ANALYT PM3 Back Off! I just backed up a.edr to ./#a.edr.5#Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps = 1000counting the number of NH-C=O groupsMPI process rank 0 (n0, p18041) caught a SIGSEGV. and here is the end of my md.log file Initializing LINear Constraint Solver number of constraints is 6 average number of constraints coupled to one constraint is 0.0 Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps = 1000 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.098311 1707 1710 0.093123 After LINCS 0.03 1684 1687 0.01 Going to use C-settle (1267 waters)wo = 0.33, wh =0.33, wohh = 3, rc = 0.08165, ra = 0.0384897rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1Grid: 9 x 9 x 6 cellsConfiguring nonbonded kernels...Testing AMD 3DNow support... not present.Testing ia32 SSE support... present. I do not have any idea why this is happening?.May I ask you what does it means?Any help will be greatly appreciatedKarim MahnamInstitute of Biochemistry and Biophysics (IBB)Tehran University P.O.box 13145-1384Tehran Iran http://www.ibb.ut.ac.ir/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
