[gmx-users] LINCS warning on galactose molecule
Dear gmx-users, I'm experimenting a LINCS warning on my system, an enzyme with ATP, galactose and Mg. We started from the crystallographic structure, made some accommodation on the topology of the sugar in order to check for partial charges (according to Justin Lemkul's suggestions on PRODRG server), then performed a minimization, NVT and NPT PR-MD and the production MD. After about 5 ns of simulation the MD stopped with the LINCS error: Step 2562553, time 5125.11 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000102, max 0.001903 (between atoms 7643 and 7642) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 45.3 0.1000 0.1000 0.1000 Step 2562554, time 5125.11 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000104, max 0.001558 (between atoms 7643 and 7642) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 36.5 0.1000 0.1000 0.1000 Step 2562565, time 5125.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000318, max 0.007712 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 31.5 0.1005 0.1008 0.1000 Step 2562566, time 5125.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000374, max 0.009231 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 38.2 0.1008 0.1009 0.1000 Step 2562567, time 5125.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000310, max 0.007658 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 38.6 0.1009 0.1008 0.1000 Step 2563563, time 5127.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.70, max 0.001640 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 57.0 0.0998 0.1002 0.1000 --- Program mdrun, VERSION 4.0.3 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1000) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem --- We checked the system to find the problem. The atoms 7641 and 7640 correspond to atom O1 and H12 of the galactose. With VMD we visualized the trajectory, but we did not see anything anomalous on this bond. Length and angles are quite normal. This OH group is near the phosphate of ATP but the distances seem to be compatible with an (expected) H-bond. I don't think the problem could be an incorrect stabilization because it seems to me that in that case the problem would have appear during the first step of MD, not after 5 ns. In any case, stabilization went correctly, with no errors or warnings. I checked on the gmx-users list and found some messages of Xavier Periole experimenting some LINCS problems with gmx 4.0.4, that seems to resemble my situation. I followed the thread, but I did not see anything that could be of help for me. Some hypotheses were about the gmx version (mine is 4.0.3), communications between CPUs, virtual sites. Looking at the trajectory, I don't think it's a problem of periodic images too close. The thread stops with Xavier saying he would like to test the effects of using -rdd and -rcon on LINCS warning, but I did not find the rest of the history. Does anybody (and especially Xavier, if possible!) have some hints about my problem? Or could it be a problem of galactose topology? Thank you very much and best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with the gun is a dead man -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS warning on galactose molecule
On 23/03/2011 9:45 PM, Anna Marabotti wrote: Dear gmx-users, I'm experimenting a LINCS warning on my system, an enzyme with ATP, galactose and Mg. We started from the crystallographic structure, made some accommodation on the topology of the sugar in order to check for partial charges (according to Justin Lemkul's suggestions on PRODRG server), then performed a minimization, NVT and NPT PR-MD and the production MD. After about 5 ns of simulation the MD stopped with the LINCS error: Step 2562553, time 5125.11 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000102, max 0.001903 (between atoms 7643 and 7642) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 45.3 0.1000 0.1000 0.1000 Step 2562554, time 5125.11 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000104, max 0.001558 (between atoms 7643 and 7642) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 36.5 0.1000 0.1000 0.1000 Step 2562565, time 5125.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000318, max 0.007712 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 31.5 0.1005 0.1008 0.1000 Step 2562566, time 5125.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000374, max 0.009231 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 38.2 0.1008 0.1009 0.1000 Step 2562567, time 5125.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000310, max 0.007658 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 38.6 0.1009 0.1008 0.1000 Step 2563563, time 5127.13 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.70, max 0.001640 (between atoms 7641 and 7640) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 7641 7640 57.0 0.0998 0.1002 0.1000 --- Program mdrun, VERSION 4.0.3 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (1000) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem --- We checked the system to find the problem. The atoms 7641 and 7640 correspond to atom O1 and H12 of the galactose. With VMD we visualized the trajectory, but we did not see anything anomalous on this bond. Length and angles are quite normal. This OH group is near the phosphate of ATP but the distances seem to be compatible with an (expected) H-bond. I don't think the problem could be an incorrect stabilization because it seems to me that in that case the problem would have appear during the first step of MD, not after 5 ns. In any case, stabilization went correctly, with no errors or warnings. I checked on the gmx-users list and found some messages of Xavier Periole experimenting some LINCS problems with gmx 4.0.4, that seems to resemble my situation. I followed the thread, but I did not see anything that could be of help for me. Some hypotheses were about the gmx version (mine is 4.0.3), communications between CPUs, virtual sites. Looking at the trajectory, I don't think it's a problem of periodic images too close. The thread stops with Xavier saying he would like to test the effects of using -rdd and -rcon on LINCS warning, but I did not find the rest of the history. Does anybody (and especially Xavier, if possible!) have some hints about my problem? Or could it be a problem of galactose topology? Usually the problem has nothing to do with LINCS or -rdd or -con - they're just symptoms of machinery that breaks first. I'd start by assuming my topologies were not well-formed somehow, and divide and conquer to locate the problem. Can you simulate galactose in vacuo? In a small water box? Same for ATP. Same for enzyme. Mark -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
