Re: [gmx-users] Stabilizing a heavy metal ion in solution
On 13/07/2010 3:52 PM, Francisco Garcia wrote: Dear users, I would like to know if users can give me a couple of suggestions on how to control large temperature swings of a heavy metal ion like Uranium in solution. The temperature of the metal ion fluctuates considerably and hardly stabilizes--even in the long time limit while the solvent temperature stabilizes easily. The gromacs 'what not to do" list strongly discourages against coupling the ion and solvent to separate thermostats. I would like to know if experienced users can give tips on how to alleviate this problem. Probably the variation you are seeing is that expected for a single atom - temperature depends on the average KE, of course. The temperature of the solvent is being averaged over many more atoms, and unsurprisingly has lower fluctuations. You could measure the temperature of a single water molecule to see how that compares. 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/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/mailing_lists/users.php
[gmx-users] Stabilizing a heavy metal ion in solution
Dear users, I would like to know if users can give me a couple of suggestions on how to control large temperature swings of a heavy metal ion like Uranium in solution. The temperature of the metal ion fluctuates considerably and hardly stabilizes--even in the long time limit while the solvent temperature stabilizes easily. The gromacs 'what not to do" list strongly discourages against coupling the ion and solvent to separate thermostats. I would like to know if experienced users can give tips on how to alleviate this problem. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: grommp_md error
Moeed: I think you make the things more complicated than they really are. > 2- I have a question about doing NPT for compressing the system. Can I also > do NVT for a short time and when the chain has a more realistic structure , > take that structure and change the volume myself? I am just asking for the > sake of learning.. This doesnt mean I am not going to do follow your > advise.. You should compress the system in such a way that it becomes a bit smaller than you need. Then one can "enlarge" the system in the GRO file (or using editconf) if needed. For running such MD runs, you should use your complete system, not the elementary cell, certainly. As for me, I think you do not need NVT at all. > 3- Also If I want to find the pressure which gives the size I want, I need > to wait till the end of simulation to see the volume (eg with g_energy) and > repeat this to find the desired volume by try and error? I think you can plot system volume vs pressure using multiple NPT runs. Best. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grommp_md error
Moeed wrote: Hello, Sorry I did not paste the error message part properly. Initially I am trying to study PE in vacuum (current box size 30*30*30 nm) and then I will solvate the PE with Hexane. NOTE 1 [file md-July11-NPTcompression.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Opening library file /chem_soft/gromacs/share/gromacs/top/spc.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'polymer' processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat Making dummy/rest group for Acceleration containing 2896 elements Making dummy/rest group for Freeze containing 2896 elements Making dummy/rest group for Energy Mon. containing 2896 elements Making dummy/rest group for VCM containing 2896 elements Number of degrees of freedom in T-Coupling group Eth is 5373.22 Number of degrees of freedom in T-Coupling group EthB is 211.89 Number of degrees of freedom in T-Coupling group EthE is 211.89 Making dummy/rest group for User1 containing 2896 elements Making dummy/rest group for User2 containing 2896 elements Making dummy/rest group for XTC containing 2896 elements Making dummy/rest group for Or. Res. Fit containing 2896 elements Making dummy/rest group for QMMM containing 2896 elements T-Coupling has 3 element(s): Eth EthB EthE Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... writing run input file... There was 1 note There was 1 warning --- Program grompp, VERSION 4.0.7 Source code file: gmx_fatal.c, line: 481 Fatal error: Too many warnings (1), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. --- "My Heart is Just a Muscle In a Cavity" (F. Black) :-) G R O M A C S (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (double precision) (-: processing topology... turning all bonds into constraints... Analysing residue names: There are: 240 OTHER residues There are: 0PROTEIN residues There are: 0DNA residues Analysing Other... This run will generate roughly 14 Mb of data * Then I altered the tc groups in mdp file to Polymer and use n option in grompp. Do you understand why you're doing this? Or are you just trying to follow some other advice that's been taken out of context? grompp -f md-July11-NPTcompression.mdp -c PE60_b4pr -p PE60.top -o PE60_md -n index.ndx >& output.grompp_md (actually I wanted to what how tc group names are based on? I thought they come from residue names, then I changed index file [all] name to You should read about thermostats in the manual, relevant literature, and perhaps some textbooks before you do anything else. If you have a single polymer molecule in vacuum, you do not need any special groups, just "System." If the reasons for this are unclear to you, stop and read before doing anything else, or you're going to waste a lot of time. [polymer] index file: [ special ] 1 3 [ Polymer ] 1 2 3 4 T
[gmx-users] grommp_md error
Hello, Sorry I did not paste the error message part properly. Initially I am trying to study PE in vacuum (current box size 30*30*30 nm) and then I will solvate the PE with Hexane. NOTE 1 [file md-July11-NPTcompression.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Opening library file /chem_soft/gromacs/share/gromacs/top/spc.itp Opening library file /chem_soft/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'polymer' processing coordinates... double-checking input for internal consistency... Velocities were taken from a Maxwell distribution at 300 K renumbering atomtypes... converting bonded parameters... initialising group options... processing index file... Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat Making dummy/rest group for Acceleration containing 2896 elements Making dummy/rest group for Freeze containing 2896 elements Making dummy/rest group for Energy Mon. containing 2896 elements Making dummy/rest group for VCM containing 2896 elements Number of degrees of freedom in T-Coupling group Eth is 5373.22 Number of degrees of freedom in T-Coupling group EthB is 211.89 Number of degrees of freedom in T-Coupling group EthE is 211.89 Making dummy/rest group for User1 containing 2896 elements Making dummy/rest group for User2 containing 2896 elements Making dummy/rest group for XTC containing 2896 elements Making dummy/rest group for Or. Res. Fit containing 2896 elements Making dummy/rest group for QMMM containing 2896 elements T-Coupling has 3 element(s): Eth EthB EthE Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... writing run input file... There was 1 note There was 1 warning --- Program grompp, VERSION 4.0.7 Source code file: gmx_fatal.c, line: 481 Fatal error: Too many warnings (1), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. --- "My Heart is Just a Muscle In a Cavity" (F. Black) :-) G R O M A C S (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 4.0.7 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (double precision) (-: processing topology... turning all bonds into constraints... Analysing residue names: There are: 240 OTHER residues There are: 0PROTEIN residues There are: 0DNA residues Analysing Other... This run will generate roughly 14 Mb of data * Then I altered the tc groups in mdp file to Polymer and use n option in grompp. grompp -f md-July11-NPTcompression.mdp -c PE60_b4pr -p PE60.top -o PE60_md -n index.ndx >& output.grompp_md (actually I wanted to what how tc group names are based on? I thought they come from residue names, then I changed index file [all] name to [polymer] index file: [ special ] 1 3 [ Polymer ] 1 2 3 4 error:** WARNING 1 [file md-July11-NPTcompression.mdp, line unknown]: Unknown or double left-hand 'rvw-switch' in parameter file checking input for internal consistency... NOTE 1 [file md-July11-NPTcompression.mdp, line unknown]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp Openi
Re: [gmx-users] Compile-time errors with MKL
On 13/07/10 08:20, Elton Carvalho wrote: Hello there! I'm trying to compile gromacs 4.0.7 with icc, mkl and openmpi. The problem is that, when I set the environment to LDFLAGS=-L/home/opt/intel/cmkl/10.2.5.035/lib/em64t/ -L/usr/lib CPPFLAGS=-I/home/opt/intel/cmkl/10.2.5.035/include/ and edit line 26576 of ./config to read LIBS="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core $LIBS" instead of LIBS="-lmkl $LIBS", That seems like asking for trouble. Why not set the LIBS environment variable properly before calling configure? I get the following errors in config.log: = START = configure:26570: checking for DftiComputeForward in -lmkl configure:26614: cc -o conftest -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -I/home/opt/intel/cmkl/10.2.5.035/include/ -L/home/opt/intel/cmkl/10.2.5.035/lib/em64t/ -L/usr/lib conftest.c -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lm>&5 /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_ok_to_fork' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_end_single' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_ordered' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_8' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_get_thread_num' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_barrier' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_get_num_threads' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_get_num_procs' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_4' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_end_reduce_nowait' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_critical' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_fini_8' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_serialized_parallel' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_end_critical' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_8' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `ompc_set_nested' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_get_nested' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_fini_4' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_in_parallel' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_push_num_threads' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_reduce_nowait' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_get_max_threads' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_4' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_end_serialized_parallel' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_flush' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_single' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_8' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_4' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_global_thread_num' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_end_ordered' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_fork_call' /home/opt/intel/cmkl/10.2.5.035
Re: [gmx-users] g_msd
On 13/07/10 07:22, Ricardo Cuya Guizado wrote: Dear gromacs users I make a MD of 20 ns of a solute in water With the g_msd program the msd vs the time was obtained In the plot, I observed a linear behaviour of the MSD from 0 to 15 ns and a plateau with no linear tendence at the last 5 ns arpoximately. In order to know if the observed plateau was due to the data or is due to the way as the algorithm process the data, I divided the MD in two trajectories and obtained the msd for each one. From 0-10ns, the plot observed shows a linear tendence en the begining and a plateau with no linear tendence from 9 to 10 ns. From 10-20 ns the plot observed was linear from 10 to 18 ns and not linear at the last, the same plateau was observed. Comparing the plots there are not equivalent,. Why g_msd produces a non linear plot at the last of the calculation and the plateau is ever produces. Somebody will explain the way as the g_msd algorithm work? and why the plot are no equivalent or why there must be equivalent? It's hard to offer help, because your description is incomplete. How large is the system? Should the protein be stable? What was the equilibration regime? What was the reference structure for fitting? What were your g_msd command lines? What were the MSDs reported? You should upload your plots to some free site that hosts images/files, and provide a link, rather than make a general description of them. 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/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/mailing_lists/users.php
Re: [gmx-users] g_msd
On Mon, Jul 12, 2010 at 5:22 PM, Ricardo Cuya Guizado wrote: > Dear gromacs users > I make a MD of 20 ns of a solute in water > With the g_msd program the msd vs the time was obtained > In the plot, I observed a linear behaviour of the MSD from 0 to 15 ns and a > plateau with no linear tendence at the last 5 ns arpoximately. > In order to know if the observed plateau was due to the data or is due to > the way as the algorithm process the data, I divided the MD in two > trajectories and obtained the msd for each one. > From 0-10ns, the plot observed shows a linear tendence en the begining and a > plateau with no linear tendence from 9 to 10 ns. > From 10-20 ns the plot observed was linear from 10 to 18 ns and not linear > at the last, the same plateau was observed. > Comparing the plots there are not equivalent,. > Why g_msd produces a non linear plot at the last of the calculation and the > plateau is ever produces. > Somebody will explain the way as the g_msd algorithm work? and why the plot > are no equivalent or why there must be equivalent? I will explain how the g_msd algorithm works and hopefully that will answer all your questions above. What you see in the output file is average-MSD versus time. This average is done over all the particles in the group you selected and over multiple time origins (this last option can be selected with the -trestart parameter). Also, time in column 1 is time difference from the start of your trajectory to current time. E.g., let's say you collected a trajectory over 5 time units and choose -trestart=1 time unit and -dt=1 time unit. dt=1 means you'll have 6 configurations for your analysis (including the configuration at t=0). trestart=1 means you'll have 5 distinct trajectories for your analysis: Trajectory 1: 0-5 T2: 1-5 T3: 2-5 T4: 3-5 T5: 4-5 Now you can notice that all 5 trajectories contribute to the average MSD after 1 time unit (T1-T5), 4 trajectories contribute to the average MSD after 2 time units (T1-T4), 3 trajectories to the average MSD after 3 time units (T1-T3), , and only one trajectory to the MSD after 5 time units (T1). Of course, this assumes that trestart is large enough that all all these trajectories are uncorrelated. So, it's clear that longer the time interval at which you want to evaluate the MSD lesser the number of trajectories used to evaluate it...and hence, higher error in MSD values at longer times. That might explain deviation from linear behaviour at long times. However, you must be careful in interpreting the MSD data and I recommend reading some literature on the subject. A plateau in MSD versus time data might also signify what is called cage motion, in which a particle or atom is trapped by the surrounding particles and is not able to move out of that hole on the simulation time scale. If you want you can send me your MSD versus time data along with some information on your system (such as potentials, density, temperature etc.) and I can let you know my comments. Few words of caution: Make sure that the center of mass of your particle (or atom or molecule) is diffusing several particle diameters. Also, make sure that you're calculating the self-diffusion coefficient by fitting a straight line to the linear region of MSD versus time data. You can either modify the -beginfit and -endfit options... or calculate the slope of the MSD versus time data using some other software (e.g., gnuplot, excel, etc.). If you're doing the latter you'll need to take a look at the code in gmx_msd.c to know how the diffusion coefficent is calculated from the slope of MSD versus time data (tog et correct units, use proper scaling factors, etc.). I hope that helped. -Gaurav > > > > > Regards > Ricardo Cuya > > > > > Courez la chance de voir la photo de votre coin de pays sur Bing.ca > Soumettez une photo maintenant! > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Compile-time errors with MKL
Hello there! I'm trying to compile gromacs 4.0.7 with icc, mkl and openmpi. The problem is that, when I set the environment to LDFLAGS=-L/home/opt/intel/cmkl/10.2.5.035/lib/em64t/ -L/usr/lib CPPFLAGS=-I/home/opt/intel/cmkl/10.2.5.035/include/ and edit line 26576 of ./config to read LIBS="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core $LIBS" instead of LIBS="-lmkl $LIBS", I get the following errors in config.log: = START = configure:26570: checking for DftiComputeForward in -lmkl configure:26614: cc -o conftest -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -I/home/opt/intel/cmkl/10.2.5.035/include/ -L/home/opt/intel/cmkl/10.2.5.035/lib/em64t/ -L/usr/lib conftest.c -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lm >&5 /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_ok_to_fork' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_end_single' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_ordered' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_8' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_get_thread_num' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_barrier' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_get_num_threads' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_get_num_procs' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_4' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_end_reduce_nowait' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_critical' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_fini_8' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_serialized_parallel' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_end_critical' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_8' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `ompc_set_nested' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_get_nested' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_fini_4' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_in_parallel' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_push_num_threads' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_reduce_nowait' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_get_max_threads' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_4' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_end_serialized_parallel' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_flush' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_single' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_8' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_4' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_global_thread_num' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_end_ordered' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_fork_call' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_fixed8_add' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefi
Re: [gmx-users] question about dynamics
Shuangxing Dai wrote: Thanks for the help. The error information is: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat. Do you have any idea of this information? The Berendsen method does not produce a proper ensemble for either temperature or pressure. If you want true NPT, use Parrinello-Rahman. This is all documented there are numerous threads about it in the literature and in the list archive. -Justin Thanks, Shuangxing Dai On Jul 12, 2010, at 15:43, "Justin A. Lemkul" wrote: Shuangxing Dai wrote: Hi, all: I am studying thermal expansion of bulk crystal solid. I want to reach the state with 300K in temperature and 1 bar pressure. I am not sure whether my procedure is correct or not. First I run energy minimization, then a constant volume for temperature coupling ( integrator is sd), then run with Berendson for anisotropic pressure coupling for 50 ps, then run anisotropic pressure coupling using Panello-Rahman for 10 ps, finally a constant volume step for production for 10 ps. I do not know whether this procedure is correct or not. Also, since for my small system, fluctuation is very large, so is there any way to reach the state ( 300K and 1 bar) and the system is fully in equilibrium? The timeframes you're using are extremely short. I'd suspect that it would be hard to get any system, especially a small one prone to large fluctuations, in an equilibrium state in 70 ps total. Simple equilibration of a protein in water is typically done for no less than 100 ps per ensemble. Also, I got a question about the ,mdp file options. When I use md integrator, with Nose-Hover for temperature coupling and Panello-Rahman pressure coupling, there is no error information. When I change and use Berendson for pressure coupling, there is error information and does not work. Well, what's the error? This kind of description will get you no useful advice. The error information is: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat. -Justin Anyone have idea about these? Thanks in advance. Thanks, Shuangxing Dai -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about dynamics
Thanks for the help. The error information is: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat. Do you have any idea of this information? Thanks, Shuangxing Dai On Jul 12, 2010, at 15:43, "Justin A. Lemkul" wrote: > > > Shuangxing Dai wrote: >> Hi, all: >>I am studying thermal expansion of bulk crystal solid. I want to reach >> the state with 300K in temperature and 1 bar pressure. I am not sure >> whether my procedure is correct or not. >>First I run energy minimization, then a constant volume for temperature >> coupling ( integrator is sd), then run with Berendson for anisotropic >> pressure coupling for 50 ps, then run anisotropic pressure coupling using >> Panello-Rahman for 10 ps, finally a constant volume step for production for >> 10 ps. >>I do not know whether this procedure is correct or not. Also, since for >> my small system, fluctuation is very large, so is there any way to reach the >> state ( 300K and 1 bar) and the system is fully in equilibrium? > > The timeframes you're using are extremely short. I'd suspect that it would > be hard to get any system, especially a small one prone to large > fluctuations, in an equilibrium state in 70 ps total. Simple equilibration > of a protein in water is typically done for no less than 100 ps per ensemble. > >>Also, I got a question about the ,mdp file options. When I use md >> integrator, with Nose-Hover for temperature coupling and Panello-Rahman >> pressure coupling, there is no error information. When I change and use >> Berendson for pressure coupling, there is error information and does not >> work. > > Well, what's the error? This kind of description will get you no useful > advice. The error information is: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat. > > -Justin > >> Anyone have idea about these? Thanks in advance. >> Thanks, >> Shuangxing Dai > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 listgmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_msd
Dear gromacs users I make a MD of 20 ns of a solute in water With the g_msd program the msd vs the time was obtained In the plot, I observed a linear behaviour of the MSD from 0 to 15 ns and a plateau with no linear tendence at the last 5 ns arpoximately. In order to know if the observed plateau was due to the data or is due to the way as the algorithm process the data, I divided the MD in two trajectories and obtained the msd for each one. >From 0-10ns, the plot observed shows a linear tendence en the begining and a >plateau with no linear tendence from 9 to 10 ns.From 10-20 ns the plot >observed was linear from 10 to 18 ns and not linear at the last, the same >plateau was observed. Comparing the plots there are not equivalent,. Why g_msd produces a non linear plot at the last of the calculation and the plateau is ever produces. Somebody will explain the way as the g_msd algorithm work? and why the plot are no equivalent or why there must be equivalent? Regards Ricardo Cuya _ MSN Rencontres: Faites une rencontre spéciale cette année. http://go.microsoft.com/?linkid=9734394-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fwd: dissolution of gases in liquid
In addition, we also tried to equilibrate the liquid-gas interface in the NVT and then switched on barostat. The result with barostat was unfortunately the same. I suspect the problem is in the (anisotropic) pressure coupling but I still have no idea how it can be corrected. The described setup is taken for the literature where it is reported to be successful. Vitaly -- Forwarded message -- From: Vitaly Chaban Date: Mon, Jul 12, 2010 at 10:59 PM Subject: dissolution of gases in liquid To: gmx-users@gromacs.org Hi all, We are trying to calculate the solubility of argon in water using the partial densities function. The following traditional MD setup is used. The water (=4000) is in the center of the box and is surrounded by the argon atoms (=50) along Z direction. The electrostatics is treated with PME, the LJ - with a shifted force method, the cut-offs are 0.9nm. The Parrinello-Rahman barostat is applied in Z direction only. Water and gas are coupled separately to 298K. The FFs are OK both for water and argon separately. In the NPT, a rather strange result is obtained (please see a plot) - http://yfrog.com/3mdissolj The argon atoms and the water molecules are distributed uniformly in the box and this results in the unphysically big solubility of argon. We tried also NVT (please see the above plot, http://yfrog.com/3mdissolj) and got a better situation. This one is rather physical if one considers the pressure which occurs in such setup. The question is WHY NPT gives so weird results? I would like to get the dependence of the solubility vs pressure, thus I am interested in NPT mostly. Does anybody have any insights? Vitaly Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] amber/charmm force field and HB lifetime at low temperature
Hi Mark, Thanks for your reply. I used charmm forcefield to study a solvated protein using TIP5P water model applying NVT ensemble. I did hydrogen-bond correlation function to understand the diffusivity of water near the protein. At 300K the result came out fine and comparable with the literature data but at 200K the result is not fine. I have attached the result at 200K, please find in the attachment. There you can see within 1ps there is very sharp decrease in the decay. I do not know why it is happening! Even at room temperature this result is wrong. Can you help me in the regard. Your help will be highly appreciated. Thank you. Yours sincerely, Rama On Wed, Jun 30, 2010 at 8:30 PM, Mark Abraham wrote: > > > - Original Message - > From: Ramachandran G > Date: Thursday, July 1, 2010 11:42 > Subject: [gmx-users] amber/charmm force field and HB lifetime at low > temperature > To: gmx-users@gromacs.org > > > Hi gromacs users: > > Using amber/charmm force field we simulated a solvated protein > > I've never heard of such a forcefield. What do you mean? > > > system at different temperature(300,250 and 200K). > > I used TIP5P water model and applied NVT ensemble . We analyzed the > hydrogen bond life time correlation function(HBCF) to study the protein > water interactions. At 300K, the result looks good and comparable with the > literature data. But at 250 and 200K, during the initial 0-2ps, HBCF decay > is very fast before it start to relax. > > Forcefields are typically parameterized on data around laboratory > conditions, so trying to make observations on systems whose conditions are > significantly far from those is doubtful. I don't have any real idea what > "decay is very fast before it start to relax" means, either. > > > > This problem does not arise when i tried with other force field which > came along with gromacs package(like GROMOS,OPLS..) I don't know where i am > making mistakes; patching the amber and charmm force fields to gromacs > package lead to this problem? > > 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/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/mailing_lists/users.php > HB-200K.pdf Description: Adobe PDF document -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] dissolution of gases in liquid
Hi all, We are trying to calculate the solubility of argon in water using the partial densities function. The following traditional MD setup is used. The water (=4000) is in the center of the box and is surrounded by the argon atoms (=50) along Z direction. The electrostatics is treated with PME, the LJ - with a shifted force method, the cut-offs are 0.9nm. The Parrinello-Rahman barostat is applied in Z direction only. Water and gas are coupled separately to 298K. The FFs are OK both for water and argon separately. In the NPT, a rather strange result is obtained (please see a plot) - http://yfrog.com/3mdissolj The argon atoms and the water molecules are distributed uniformly in the box and this results in the unphysically big solubility of argon. We tried also NVT (please see the above plot, http://yfrog.com/3mdissolj) and got a better situation. This one is rather physical if one considers the pressure which occurs in such setup. The question is WHY NPT gives so weird results? I would like to get the dependence of the solubility vs pressure, thus I am interested in NPT mostly. Does anybody have any insights? Vitaly Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about dynamics
Shuangxing Dai wrote: Hi, all: I am studying thermal expansion of bulk crystal solid. I want to reach the state with 300K in temperature and 1 bar pressure. I am not sure whether my procedure is correct or not. First I run energy minimization, then a constant volume for temperature coupling ( integrator is sd), then run with Berendson for anisotropic pressure coupling for 50 ps, then run anisotropic pressure coupling using Panello-Rahman for 10 ps, finally a constant volume step for production for 10 ps. I do not know whether this procedure is correct or not. Also, since for my small system, fluctuation is very large, so is there any way to reach the state ( 300K and 1 bar) and the system is fully in equilibrium? The timeframes you're using are extremely short. I'd suspect that it would be hard to get any system, especially a small one prone to large fluctuations, in an equilibrium state in 70 ps total. Simple equilibration of a protein in water is typically done for no less than 100 ps per ensemble. Also, I got a question about the ,mdp file options. When I use md integrator, with Nose-Hover for temperature coupling and Panello-Rahman pressure coupling, there is no error information. When I change and use Berendson for pressure coupling, there is error information and does not work. Well, what's the error? This kind of description will get you no useful advice. -Justin Anyone have idea about these? Thanks in advance. Thanks, Shuangxing Dai -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] question about dynamics
Hi, all: I am studying thermal expansion of bulk crystal solid. I want to reach the state with 300K in temperature and 1 bar pressure. I am not sure whether my procedure is correct or not. First I run energy minimization, then a constant volume for temperature coupling ( integrator is sd), then run with Berendson for anisotropic pressure coupling for 50 ps, then run anisotropic pressure coupling using Panello-Rahman for 10 ps, finally a constant volume step for production for 10 ps. I do not know whether this procedure is correct or not. Also, since for my small system, fluctuation is very large, so is there any way to reach the state ( 300K and 1 bar) and the system is fully in equilibrium? Also, I got a question about the ,mdp file options. When I use md integrator, with Nose-Hover for temperature coupling and Panello-Rahman pressure coupling, there is no error information. When I change and use Berendson for pressure coupling, there is error information and does not work. Anyone have idea about these? Thanks in advance. Thanks, Shuangxing Dai -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] OPLS-2005 forcefield parameters for carbohydrates in Gromacs 4.0.7?
Hello, I'm using Gromacs 4.0.7, and I'm looking for the OPLS-2005 all-atom forcefield, which I'm told contains parameters and residue topologies that will allow me to model beta (1-4) cellobiose. Does the standard OPLS-AA parameter set supplied with Gromacs 4.0.7 contain the OPLS-2005 parameters for carbohydrates (the files are labelled '2001 amino acid dihedrals') ? If so, can anyone tell me what the correct residue names are for use with cellobiose? If not, does anyone have these parameter files so I can just drop them into GMXRC? I have searched the wiki, the mailing list, and the web, but haven't found anything so far. I have found a couple of papers by Kony et al. describing the use of something called OPLS-AA-SEI for carbohydrates, but again, no actual forcefield data. I would be grateful for any help. Many thanks in advance, Steve Kirk Prof. Steven R. Kirk College of Chemistry and Chemical Engineering Hunan Normal University Changsha 40081 Hunan Province, China -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: number of degrees of frredom
= berendsen > tc-grps = Eth EthB EthE ;HEX ; groups to couple > to thermostat; Berendsen temperature coupling is on in these groups > tau_t = 0.1 0.1 0.1 ;0.1 ; time constant for > T coupling > ref_t = 300 300 300 ;300 ; reference T for > coupling. When you alter the T, don't forget to change the gen_temp for > velocity generation > > ; Pressure coupling > Pcoupl = berendsen ; Pressure coupling is not on > Pcoupltype = isotropic ; means the box expands and > contracts in all directions (x,y,z) in order to maintain the proper pressure > tau_p = 0.5 ; time constant for coupling in ps > compressibility = 4.5e-5 ; compressibility of solvent used in > simulation in 1/bar > ref_p = 1.0 ; reference P for coupling in bar > > ; Velocity generation Generate velocites is on at 300 K. > Manual p155 > gen_vel = yes ; generate velocites according to > Maxwell distribution at T: gen_temp with random gen seed gen_seed > gen_temp = 300.0 ; T for Maxwell distribution > gen_seed = 173529 ; used to initialize random > generator for random velocities > > ; Bonds > constraints = all-bonds ; sets the LINCS constraint for all > bonds > constraint-algorithm = lincs > -- next part -- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20100712/21962bb6/attachment.html > > -- > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 75, Issue 70 > * > -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] number of degrees of frredom
Moeed wrote: Dear Justin, The actual box I got by replicating monomer units has size of 15 0.5 0.5 That is chain has no space to move. I know you have already given me some tips on high repulsion in the system but that had to do with incorrect topology file. I assure you I have learned a lot from your tips ;) I'm glad to hear it. The same principal still applies, though. If a large system is failing, break it down into manageable pieces to determine where things start to break down. It is easier to solve one problem at a time than several. This time I need to have such packed system because that gives me the density I want. 0.9g/cm3 for PE! for a chain of 60 ethylene units the size should be identical to the actual size 15 0.5 0.5. And I am wondering how can I work with much longer chains ( 20 times longer)... You've been given advice about this. You probably will have to simulate within a larger box and slowly compress your system. You have constructed a linear chain of PE within a pre-defined box that gives you the density you want. Ask yourself this: is that what PE looks like, completely rigid and extended? Certainly not. The better approach would be as Vitaly and Chris have suggested - take a single molecule of PE in a very large box (forget your density for a moment) and simulate it. It will probably adopt a much more reasonable structure that you can then work with. Then slowly build up your system - 2, 4, 8 units - and it will likely be far more stable. If your box fits your system exactly, your atoms will be extremely close to one another and you will get a huge vdW repulsion. If you've learned anything from me, you should already know that I want you to break down your energy terms to see what's failing... md grompp is giving error about degrees of freedom. Any advise on this in appreciated... Thank you, md grompp aking dummy/rest group for Acceleration containing 2896 elements Making dummy/rest group for Freeze containing 2896 elements Making dummy/rest group for Energy Mon. containing 2896 elements Making dummy/rest group for VCM containing 2896 elements Number of degrees of freedom in T-Coupling group Eth is 5373.22 Number of degrees of freedom in T-Coupling group EthB is 211.89 Number of degrees of freedom in T-Coupling group EthE is 211.89 Making dummy/rest group for User1 containing 2896 elements Making dummy/rest group for User2 containing 2896 elements Making dummy/rest group for XTC containing 2896 elements Making dummy/rest group for Or. Res. Fit containing 2896 elements Making dummy/rest group for QMMM containing 2896 elements T-Coupling has 3 element(s): Eth EthB EthE Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest There is no error message here. What's the problem? mdpfile** title = PE-Hexane ;define = -DPOSRES ; tells gromacs to perform position restrained dynamics/include posre.itp into topology used for position restraint pbc = xyz; use priodic BCs in all directions ; Run control integrator = md ; type of dynamics algorithm. Here md uses a leap-frog algorithm for integrating Newtons's eq of motion dt = 0.002; in ps ! nsteps = 5000 ; length of simulation= nsteps*dt nstcomm = 1; frequency for center of mass motion removal ; Output control nstenergy = 100 ; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps nstxout = 100 ; frequency to write coordinates/velocity/force to output trajectory file. how often snapshots are collected= nstxout*dt nstvout = 100 nstfout = 0 nstlog = 100 ; frequency to write energies to log file nstxtcout = 10 ; frequency to write coordinates to xtc trajectory ; Neighbor searching nstlist = 10 ; frequency to update neighbor list. Neighborlist will be updated at least every 10 steps. Manual p80 ns_type = grid ; make a grid in the box and only check atoms in neighboring grid cells when constructing a new neighbor list every nstlist steps ; Electrostatics/VdW coulombtype = Shift; tells gromacs how to model electrostati
[gmx-users] number of degrees of frredom
Dear Justin, The actual box I got by replicating monomer units has size of 15 0.5 0.5 That is chain has no space to move. I know you have already given me some tips on high repulsion in the system but that had to do with incorrect topology file. I assure you I have learned a lot from your tips ;) This time I need to have such packed system because that gives me the density I want. 0.9g/cm3 for PE! for a chain of 60 ethylene units the size should be identical to the actual size 15 0.5 0.5. And I am wondering how can I work with much longer chains ( 20 times longer)... md grompp is giving error about degrees of freedom. Any advise on this in appreciated... Thank you, md grompp aking dummy/rest group for Acceleration containing 2896 elements Making dummy/rest group for Freeze containing 2896 elements Making dummy/rest group for Energy Mon. containing 2896 elements Making dummy/rest group for VCM containing 2896 elements Number of degrees of freedom in T-Coupling group Eth is 5373.22 Number of degrees of freedom in T-Coupling group EthB is 211.89 Number of degrees of freedom in T-Coupling group EthE is 211.89 Making dummy/rest group for User1 containing 2896 elements Making dummy/rest group for User2 containing 2896 elements Making dummy/rest group for XTC containing 2896 elements Making dummy/rest group for Or. Res. Fit containing 2896 elements Making dummy/rest group for QMMM containing 2896 elements T-Coupling has 3 element(s): Eth EthB EthE Energy Mon. has 1 element(s): rest Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1has 1 element(s): rest User2has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest mdpfile** title = PE-Hexane ;define = -DPOSRES ; tells gromacs to perform position restrained dynamics/include posre.itp into topology used for position restraint pbc = xyz; use priodic BCs in all directions ; Run control integrator = md ; type of dynamics algorithm. Here md uses a leap-frog algorithm for integrating Newtons's eq of motion dt = 0.002; in ps ! nsteps = 5000 ; length of simulation= nsteps*dt nstcomm = 1; frequency for center of mass motion removal ; Output control nstenergy = 100 ; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps nstxout = 100 ; frequency to write coordinates/velocity/force to output trajectory file. how often snapshots are collected= nstxout*dt nstvout = 100 nstfout = 0 nstlog = 100 ; frequency to write energies to log file nstxtcout = 10 ; frequency to write coordinates to xtc trajectory ; Neighbor searching nstlist = 10 ; frequency to update neighbor list. Neighborlist will be updated at least every 10 steps. Manual p80 ns_type = grid ; make a grid in the box and only check atoms in neighboring grid cells when constructing a new neighbor list every nstlist steps ; Electrostatics/VdW coulombtype = Shift; tells gromacs how to model electrostatics. Coulomb/LJ potential is decreased over the whole range and forces decay smoothly to zero betw$ vdw-type= Shift; rcoulomb-switch/rvw-switch & rcoulomb/rvdw rcoulomb-switch = 0; where to start switching the Coulomb potential rvw-switch = 0; where to start switching the LJ potential ; Cut-offs rlist = 1.1 ; in nm. Cut-off distance for short-range neighbor list rcoulomb= 1.0 ; distance for coulomb cut-off rvdw= 1.0 ; distance for coulomb cut-off ; Temperature coupling Tcoupl = berendsen tc-grps = Eth EthB EthE ;HEX; groups to couple to thermostat; Berendsen temperature coupling is on in these groups tau_t = 0.1 0.1 0.1 ;0.1; time constant for T coupling ref_t = 300 300 300 ;300; reference T for coupling. When you alter the T, don't forget to change the gen_temp for velocity generation ; Pressure coupling Pcoupl = berendsen; Pressure coupling is not on Pcoupltype= isotropic ; means the box expands and contracts in all directions (x,y,z) in
Re: [gmx-users] -tu flag in g_hbond
shahab shariati wrote: Dear Justin I opened my hbmap.xpm file by a text editor. first of file is as follows : /* XPM */ /* Generated by g_hbond */ /* This file can be converted to EPS by the GROMACS program xpm2ps */ /* title: "Hydrogen Bond Existence Map" */ /* legend: "Hydrogen Bonds" */ /* x-label: "Time (ns)" */ /* y-label: "Hydrogen Bond Index" */ /* type:"Discrete" */ I changed x-label: "Time (ps)" to x-label: "Time (ns)" . but only label of x-axis was changed. please guide me There should be a line further down that contains the actual time, labeled with "x-axis." Those are the values you need to change in order for the time to show up as ns, otherwise all you've done is label times in ps as ns. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] -tu flag in g_hbond
Dear Justin *excuseme this email is true.* I opened my hbmap.xpm file by a text editor. first of file is as follows : /* XPM */ /* Generated by g_hbond */ /* This file can be converted to EPS by the GROMACS program xpm2ps */ /* title: "Hydrogen Bond Existence Map" */ /* legend: "Hydrogen Bonds" */ /* x-label: "Time (ps)" */ /* y-label: "Hydrogen Bond Index" */ /* type:"Discrete" */ I changed x-label: "Time (ps)" to x-label: "Time (ns)" . but only label of x-axis was changed. please guide me -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] -tu flag in g_hbond
Dear Justin I opened my hbmap.xpm file by a text editor. first of file is as follows : /* XPM */ /* Generated by g_hbond */ /* This file can be converted to EPS by the GROMACS program xpm2ps */ /* title: "Hydrogen Bond Existence Map" */ /* legend: "Hydrogen Bonds" */ /* x-label: "Time (ns)" */ /* y-label: "Hydrogen Bond Index" */ /* type:"Discrete" */ I changed x-label: "Time (ps)" to x-label: "Time (ns)" . but only label of x-axis was changed. please guide me -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: selenium parameter
Susan. Please use the mailing list instead of personal email. A google search for electronegativity of selenium provides a useful first hit. The .rtp issue is covered often on the mailing list. Overall, you will find this link helpful: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette Quoting Susan COSTANTINI : Dear Chris I have read your mail regarding the selenium parameters and I have tried to insert the SEG atom in ffG43a1.rtp but Gromacs gives error. Where I can the electronegativities of Se? When I run the pdb2gmx comand, Gromacs give this error: --- Program pdb2gmx, VERSION 3.3.3 Source code file: pdb2gmx.c, line: 421 Fatal error: Atom SEG in residue CYSH 50 not found in rtp entry with 8 atoms while sorting atoms --- Have you idea how I can solve this problem? Thank you in advance!! Susan Costantini Senior Fellow Oncologic Center Research in Mercogliano (Italy) I don't have the parameters. You could possibly fudge it by extrapolating out from SER->CYS->Se_CYS based scaled by electronegativities of O,S,Se. I'm not saying that this is rigorous, just that its possible to do. My main point here, though, is to ask if you *really* need to bother with this. Thioredoxin ~ 100 amino acids. Sampling is a real problem in simulations, and I highly doubt that you're going to see a difference in CYS vs. Se_CYS in the context of a 100 aa protein on simulation timescales (I also doubt you'd see a difference for CYS vs. SER). Besides, wouldn't crystallographers be basically out of business if Se_CYS mucked up the structure as compared to CYS? Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] -tu flag in g_hbond
shahab shariati wrote: Dear Justin thanks for your attention. this file that I want to be as ns is hbmap.xpm I did following steps to obtain pdf file : 1) xpm2ps 2) ps2pdf can I open xpm file by xmgrace? No, you'll have to edit it by hand in a text editor. I was assuming you wanted .xvg output. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] -tu flag in g_hbond
Dear Justin thanks for your attention. this file that I want to be as ns is hbmap.xpm I did following steps to obtain pdf file : 1) xpm2ps 2) ps2pdf can I open xpm file by xmgrace? -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] -tu flag in g_hbond
shahab shariati wrote: Hi gromacs users in g_hbond command there is not -tu flag and I want to have time unit as ns no default form (ps). What is the best way to do this? Please suggest. Either modify the code or simply change the axis labels in xmgrace. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] -tu flag in g_hbond
Hi gromacs users in g_hbond command there is not -tu flag and I want to have time unit as ns no default form (ps). What is the best way to do this? Please suggest. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: ffamber99sb error
Arik: Your topology file(s) are welcome in order to provide help. Vitaly > I'll be most thankful for any comment/help you might have regarding the > following error that I'm encountering in grompp_d : > > Atomtype amber99_34 not found > > In ffamber99sb.rtp, amber99_34 refers to the N atom of each amino acid. > > Thanks a lot > > Arik -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: MD run for octanol system
Hmm... Straight lines... Is it VMD that your used to visualize the trajectory? I think this is just due to PBC. Compute some RDFs and they will give you an answer if your system is healthy. Dr. Vitaly Chaban > I am trying to run MD simulation for octanol using GROMACS, I have > downloaded the octanol.tar.gz from the user contributed section > http://www.gromacs.org/@api/deki/files/18/=octanol.tar.gz. > When I performed this MD run according to the run input file and molecule > topology provided in this download, I observed straight lines in the system > while visualizing the trajectory. Can anybody suggest if there is any > problems in the run parameters provided or it is some mistake at my part ? > As a first thought It seems like a boundary condition problem to me. Any > insight into this will be really helpful for me. > Is there any other source for getting required information for octanol. > My final target is to run MD in water/octanol box. Please guide me with dos > and donts, If anybody has attempted for the same. -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Where can I dowload DSSP program?
Hello This link will help - http://swift.cmbi.ru.nl/gv/dssp Regards Ajeeta On Mon, Jul 12, 2010 at 3:41 PM, chandran karunakaran wrote: > Hi GMX users, > >I am interested in doing dssp analysis. Where can I > download dssp program? I apprecitate if you could send > the web address for it. > > with thanks > ***+ > Dr.Karunakaran Chandran + > Biophysics Department + > Medical College of Wisconsin + > Milwaukee, WI-53226 + > Resi.: 414-443-0085 + > Off : 414-456-4034 + > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Where can I dowload DSSP program?
Hi GMX users, I am interested in doing dssp analysis. Where can I download dssp program? I apprecitate if you could send the web address for it. with thanks ***+ Dr.Karunakaran Chandran+ Biophysics Department + Medical College of Wisconsin + Milwaukee, WI-53226+ Resi.: 414-443-0085+ Off : 414-456-4034+ -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] MD run for octanol system
Hi, try converting (trjconv) your trajectory using the flag "-pbc res" or "-pbc mol" Esteban -- On Mon, Jul 12, 2010 at 8:45 AM, vivek sharma wrote: > Hi There, > I am trying to run MD simulation for octanol using GROMACS, I have > downloaded the octanol.tar.gz from the user contributed section > http://www.gromacs.org/@api/deki/files/18/=octanol.tar.gz. > When I performed this MD run according to the run input file and molecule > topology provided in this download, I observed straight lines in the system > while visualizing the trajectory. Can anybody suggest if there is any > problems in the run parameters provided or it is some mistake at my part ? > As a first thought It seems like a boundary condition problem to me. Any > insight into this will be really helpful for me. > Is there any other source for getting required information for octanol. > My final target is to run MD in water/octanol box. Please guide me with dos > and donts, If anybody has attempted for the same. > > Thanks in advance!!! > > regards, > Vik > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: g_cluster settings
Marc - Note that you used the linkage method which maps a structure to a cluster if its distance to any structure already in the cluster is is less than the cutoff. If you think it's not representative of your system try another clustering method, but note that you may need a longer trajectory as well. Vitali - g_clustersize is for clustering molecules (can be useful e.g., for the formation of micelles) whereas g_cluster is for clustering the trajectories. Ran Vitaly Chaban wrote: > Dear Marc: > > Please look towards g_clustzise (instead of g_cluster). We tried to > use g_cluster some years ago and eventually switched to g_clustzise - > I do not remember why but the latter was more successful. If you want > to monitor the number of clusters in the system, g_clustzise can > certainly do it. > > Dr. Vitaly Chaban > > > > >> I am trying to perform a cluster analysis on a 4 ns trajectory (4000 >> frame >> trajectory), but I am not getting any more than 1 cluster until I get down >> to a >> cutoff of 0.05 nm. This seems like an awfully small number, so I checked my >> rmsd >> distribution and found that 44% of my rmsds are at 0.1 nm or greater. My >> distribution looks like the following: >> >> And my command line is as follows: >> >> g_cluster -f md.trr -s md.tpr -n index.ndx -sz clustersize1.xvg -clid >> clusterid1.xvg -cutoff .10 -cl clusters1.pdb -b 1 -e 4001 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
