[gmx-users] Something wrong with the force field parameter
Dear all, I am now running the MD simulation for a small molecular not covered by the rtp file. The force field I used is oplsaa. I genereated the gro and top file using PRODRG program (from its website). and added them to the ffoplsaa.rtp ffoplsaa.hdb. Finally I got the gro and top file for my small molecular. But when I run the energy minimization for this molecular, the atoms detached and run out of the bond range. There must be something wrong with the force field parameter. Would you kindly show me, how to generate the force field parameter for the oplsaa? Thanks SUN,Jian ___ 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] pdb2gmx error, How to generate the gro and top file for a small molecular?
Dear all, I am doing the simulation of a protein with a small molecular in its active site. But unfortunately, pdb2gmx cannot generate the gro and top file for the small molecualr? I am using the oplsaa force field, who can tell me how to generate the gro and top files? Thanks a lot Jian ___ 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] Help! LINCS WARNING errors.
Dear Dr. David van der Spoel, Thanks for your reply. 1. I didn't set conservation for energy, nor p_couple for my system. 2. You said bad structures, Do you mean my system is not fully equilibrium? Or my protein structure is totally wrong? I am trying to spend more simulation time on equilibrium for the system, will it help? I searched the mail list archives for simulated annealing. But there are so many mails on this topic and most of them are not replied or solved. Maybe we should have some volunteer to classify the archives and update the FAQ. That would be very helpful for newbies like me. :-) Thanks Regards, Jian SUN, Jian wrote: Dear all, I am running simulated annealing for a protein in water and found something strange: 1. the poteintial energy keep on rising while the system is cooling down conservation of energy? 2. several LINCS WARNINGs are given (I have posted the question but no reply till now) and then the energies become nan bad structures. check mailing list archives. Who can tell me why? Thanks a lot. ___ 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] Help! LINCS WARNING errors.
Dear all, I am running simulated annealing for a protein in water and found something strange: 1. the poteintial energy keep on rising while the system is cooling down 2. several LINCS WARNINGs are given (I have posted the question but no reply till now) and then the energies become nan Who can tell me why? Thanks a lot. the following is part of my logfile. Constraint error in algorithm Lincs at step 263645 t = 263.645 ps: Water molecule starting at atom 70574 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates Step Time Lambda 263700 263.70001 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.00 1 2 nan After LINCS 0.00 1 2 nan Current ref_t for group rest: 250.3 Energies (kJ/mol) Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 nan nan nan nan nan LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy 0.0e+00 0.0e+00 nan nan nan Temperature Pressure (bar) nan nan Step Time Lambda 263800 263.80002 0.0 Rel. Constraint Deviation: Max between atoms RMS Before LINCS 0.00 1 2 nan After LINCS 0.00 1 2 nan ___ 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] LINCS WARNING max 2022834176.000000 (between atoms 5655 and 5658) rms 81089176.000000
Dear all, I am running the simulated annealing for a protein solvented in a water box, but I get such LINCS WARNING as max 2022834176.00 (between atoms 5655 and 5658) rms 81089176.00 Why? Does it mean that my system is exploring? The following is my mdp file and some of the LINCS WARNING message: dt = 0.001 ; SIMULATED ANNEALING annealing = single annealing_npoints = 3 annealing_time = 0 50 800 annealing_temp = 0 350 0 gen_vel = no gen_temp = 0 gen_seed = 173529 constraints = all-bonds constraint_algorithm = lincs lincs_order = 4 lincs_iter = 2 Step 263643, time 263.643 (ps) LINCS WARNING relative constraint deviation after LINCS: max 2022834176.00 (between atoms 5655 and 5658) rms 81089176.00 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 190 192 32.5 0.1336 0.1773 0.1335 192 193 47.2 0.1011 0.1537 0.1010 ... 5643 5646 151.3 2714.9613 68555.9304 0.1529 5646 5647 65.9 1894.6184 216204.0509 0.1090 5646 5648 69.8 1818.5108 212516.4615 0.1090 5649 5650 173.5 447425.3856 22302675.1767 0.1229 5649 5651 156.8 1680664.1544 50630117.0698 0.1335 5651 5652 146.9 1789339.4529 46335793.8246 0.1010 5651 5653 174.1 5949343.3105 149770966.9350 0.1449 5653 5654 171.6 7324940.0095 183521837.1456 0.1090 5653 5655 177.6 16072804.7240 243272781.1728 0.1529 5653 5669 178.4 5469409.9743 152675417.1142 0.1522 5655 5656 177.8 18428095.3131 204639707.3293 0.1090 5655 5657 176.6 18485738.1080 204477063.8333 0.1090 5655 5658 179.1 30390583.4845 305447945.4836 0.1510 5658 5659 179.2 30123192.5220 273034063.5045 0.1400 5658 5661 178.6 29490165.1653 271759183.7457 0.1400 5659 5660 176.4 17471940.7463 154679010.3056 0.1080 5659 5663 178.5 16208110.3050 148729415.1683 0.1400 5661 5662 177.2 16669061.9731 152805630.9454 0.1080 5661 5665 177.7 14573623.8544 146053907.4077 0.1400 5663 5664 177.0 9332011.5148 90334896.9046 0.1080 5663 5667 176.5 9190421.7390 97130164.6485 0.1400 5665 5666 175.0 8010325.5108 87779001.5722 0.1080 .. ___ 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] How to use the simulated annealing porotocal of gromacs 3.3?
Dear all, I am trying to use the simulated annealing porotocal of gromacs 3.3 (single precision) to find the global energy minimization of a protein in a water box. I set the mdp file as follow: ; VARIOUS PREPROCESSING OPTIONS title= Simulation ; Preprocessor - specify a full path if necessary. cpp = cpp include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 100 ;1000ps ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing= periodic ; Number of time points to use for specifying annealing in each group annealing_npoints= 4 ; List of times at the annealing points for each group annealing_time = 0 2 8 14 ; Temp. at each annealing point, for each group. annealing_temp = 270 270 330 270 gen_vel = yes gen_temp = 270 gen_seed = 173529 constraints = all-bonds constrain_algorithm = lincs linvd_order = 4 = but the run procedure kept on crashing. I checked the trr file and log file, and found the energy(potential energy and total energy) kept on increasing in spite of the temperture is fluctuating between 270K and 330K. Why? Should I set some parameters for constant pressure? I would be very grateful if you can give me some suggestion. Thanks, Kino ___ 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
