[gmx-users] Error when extending simulation
Hi Gromacs user, when I try to extend on of my simulations with mdrun -deffnm pdz_cis_NVT_disre_equi_3 -cpi pdz_cis_NVT_disre_equi_3.cpt -append I get the following error Fatal error: Count mismatch for state entry disre_rm3tav, code count is 0, file count is 13 and have no idea whats wrong. Any suggestion is very much appreciated Yours Sebastian -- 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] Re: gInstallation Problems with Gromacs4.6
OK, but that still might not be fixing the real problem, which might be
starting with how you are calling cmake in the first place.
Mark
On Sat, Mar 2, 2013 at 7:20 AM, Abhishek Acharya aacha...@iitk.ac.inwrote:
Date: Fri, 1 Mar 2013 23:59:36 +0530
From: Abhishek Acharya aacha...@iitk.ac.in
Subject: [gmx-users] Installation Problems with Gromacs4.6
To: gromacs maillist gmx-users@gromacs.org
Message-ID:
2ca7063e41d6ddfa7ea411dc3cfe3ad3.squir...@webmail.iitk.ac.in
Content-Type: text/plain;charset=iso-8859-1
Hello Gromacs Users.
I have been trying to install Gromacs4.6 on our HPC facility. I think I
have correctly provided all the necessary mpi and fftw library paths.
But
when i try to run configure it gives me the following error:
CMake Error at cmake/FindFFTW.cmake:105 (message):
Could not find fftwf_plan_r2r_1d in
/home/aacharya/softwares/fftw-3.3.3/lib/libfftw3f.so, take a look at
the
error message in
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeError.log
to
find out what went wrong. If you are using a static lib (.a) make
sure
you
have specified all dependencies of fftw3f in FFTWF_LIBRARY by hand
(e.g.
-DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):
CMakeLists.txt:894 (find_package)
As suggested here I looked into the CMakeError.log file of which I can't
make any sense.
Source file was:
#include mpi.h
int main(void) {
void* buf;
MPI_Allreduce(MPI_IN_PLACE, buf, 10, MPI_FLOAT, MPI_SUM,
MPI_COMM_WORLD);
}
Determining if the function fftwf_plan_r2r_1d exists in the
/home/aacharya/softwares/fftw-3.3.3/lib failed with the following
output:
Change Dir:
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/gmake cmTryCompileExec2668319475/fast
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec2668319475.dir/build.make
CMakeFiles/cmTryCompileExec2668319475.dir/build
gmake[1]: Entering directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E
cmake_progress_report
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp/CMakeFiles
1
Building C object
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d -o
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -c
/home/aacharya/softwares/cmake-2.8.10.2/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec2668319475
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_link_script
CMakeFiles/cmTryCompileExec2668319475.dir/link.txt --verbose=1
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d
-L/home/aacharya/softwares/fftw-3.3.3/lib
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -o
cmTryCompileExec2668319475 -rdynamic -lm
Strange, there is supposed to be a -lfftw3f before -lm. Can you
tell us what your cmake command line was?
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o: In
function `main':
CheckFunctionExists.c:(.text+0x15): undefined reference to
`fftwf_plan_r2r_1d'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTryCompileExec2668319475] Error 1
gmake[1]: Leaving directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec2668319475/fast] Error 2
Kindly help. I tried installing 4.5.6 and it got installed without any
such problems. I need 4.6 because my tpr files are produced in
Gromacs4.6
and I am using the Verlet cutoff scheme.
Thank you Mark and Christoph for your replies. I solved the installation
problem by configuring gromacs with static libraries. I somehow didn't
notice earlier, there was a note saying that Shared Libraries might be
problematic with MPI.
With Regards
Abhishek
--
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Re: [gmx-users] Thread affinity setting failed
On Mon, Mar 4, 2013 at 6:02 AM, Reid Van Lehn rvanl...@mit.edu wrote: Hello users, I ran into a bug I do not understand today upon upgrading from v. 4.5.5 to v 4.6. I'm using older 8 core Intel Xeon E5430 machines, and when I submitted a job for 8 cores to one of the nodes I received the following error: NOTE: In thread-MPI thread #3: Affinity setting failed. This can cause performance degradation! NOTE: In thread-MPI thread #2: Affinity setting failed. This can cause performance degradation! NOTE: In thread-MPI thread #1: Affinity setting failed. This can cause performance degradation! I ran mdrun simply with the flags: mdrun -v -ntmpi 8 -deffnm em Using the top command, I confirmed that no other programs were running and that mdrun was in fact only using 5 cores. Reducing -ntmpi to 7, however, resulted in no error (only a warning about not using all of the logical cores) and mdrun used 7 cores correctly. Since it warned about thread affinity settings, I tried setting -pin on -pinoffset 0 even though I was using all the cores on the machine. This resulted in the same error. However, turning pinning off explicitly with -pin off (rather than -pin auto) did correctly give me the all 8 cores again. While I figured out a solution in this particular instance, my question is whether I should be have known from my hardware/settings that pinning should be turned off (for future reference), or if this is a bug? I'm not sure - those are 2007-era processors, so there may be some limitations in what they could do (or how well the kernel and system libraries support it). So investing time into working out the real problem is not really worthwhile. Thanks for reporting your work-around, however, others might benefit from it. If you plan on doing lengthy simulations, you might like to verify that you get linear scaling with increasing -ntmpi, and/or compare performance with the MPI version on the same hardware. 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
[gmx-users] H-D-A angle in H-bond
Dear GROMACS users, In gromacs, the default values of the geometrical criterion of H-bond are 0.35 nm and 30 deg for spc water molecules. The acceptor and donor atoms of H-bond in my system are different than in the water system. Therefore I think that I should use suitable D-A distance and H-D-A (alpha) angle for my system in order to calculate the number of H-bond. I obtained the D-A distance and the A-H-D angle from Cambridge Structural Database (CSD) but I couldn’t find the H-D-A angle from CSD. I want to learn how I can obtain the H-D-A (alpha) angle. If you can answer me, I’ll be so glad. Dr. M. Capar -- View this message in context: http://gromacs.5086.n6.nabble.com/H-D-A-angle-in-H-bond-tp5006072.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
[gmx-users] X particles communicated to PME node Y are more ...
Dear gmx users, I have successfully performed simulations on a charged peptide. I did a series of mutations and everything had a happy end. Now I have tried another mutation (just substitution of Asn to Lys) and I am getting the well-known X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group message error during energy minimization, right at the beginning (step 0). My energy minimization mdp file looks as follows: integrator = steep ; emtol = 1000.0; emstep = 0.02 ; nsteps = 7 ; nstlist = 1 ; ns_type = grid; rlist = 1.0 ; coulombtype = PME ; rcoulomb= 1.0; rvdw= 1.0 ; pbc = xyz; I have tried without neutralizing with ions, changing the time step, changing the integrator and the values for rcoulomb,rlist, etc. I have changed all the parameteres in the mdp file and I get a smaller value of particles in the message error, but still a crash. The box size has also no effect on the message error. I have checked the starting structure and everything is fine. Mutating that Asn to a non-charged residue does not yield any problem, but I want to study the effect in the Asn-- Lys mutation. Any hint to solve the error? -- 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
[gmx-users] Difference in Number of contacts through g_hbond and g_mindist
Hi All, I have a doubt regarding the calculation of number of contacts between two groups. Because, I am getting different number of contacts calculated through g_hbond -contact option and g_mindist -on option. I have used same cutoff for distance (0.6nm) in both the cases. -- *--- Thanks and Regards, Bipin Singh* -- 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] Switching functions for only some molecules
On 3/4/13 12:50 AM, Jeff Yew wrote: If I have water and solvent, and I only want to apply a short range switching function to the water - water interactions (not solvent - solvent or water - solvent), is it possible in Gromacs? I am interested in reproducing TIP4P-EW water. If I add coulombtype = PME-Switch and vdwtype = Switch in the mdp file, it will apply to all interactions. You can't apply different nonbonded schemes to different elements of your system using .mdp options. Try tabulated potentials. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] H-D-A angle in H-bond
On 3/4/13 7:54 AM, mcapar wrote: Dear GROMACS users, In gromacs, the default values of the geometrical criterion of H-bond are 0.35 nm and 30 deg for spc water molecules. The acceptor and donor atoms of H-bond in my system are different than in the water system. Therefore I think that I should use suitable D-A distance and H-D-A (alpha) angle for my system in order to calculate the number of H-bond. I obtained the D-A distance and the A-H-D angle from Cambridge Structural Database (CSD) but I couldn’t find the H-D-A angle from CSD. I want to learn how I can obtain the H-D-A (alpha) angle. If you can answer me, I’ll be so glad. The default settings do not apply just to SPC; in fact, they come from average values obtained from crystallographic databases. There are a few threads with fairly extensive discussions on this topic. Most papers that I see use similar, if not identical, settings to g_hbond. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] X particles communicated to PME node Y are more ...
On 3/4/13 8:25 AM, Miguel Ángel Mompeán García wrote: Dear gmx users, I have successfully performed simulations on a charged peptide. I did a series of mutations and everything had a happy end. Now I have tried another mutation (just substitution of Asn to Lys) and I am getting the well-known X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group message error during energy minimization, right at the beginning (step 0). My energy minimization mdp file looks as follows: integrator = steep ; emtol = 1000.0; emstep = 0.02 ; nsteps = 7 ; nstlist = 1 ; ns_type = grid; rlist = 1.0 ; coulombtype = PME ; rcoulomb= 1.0; rvdw= 1.0 ; pbc = xyz; I have tried without neutralizing with ions, changing the time step, changing the integrator and the values for rcoulomb,rlist, etc. Bad idea. Nonbonded cutoffs are an intrinsic part of the force field. Changing them will actually increase your likelihood of failure. I have changed all the parameteres in the mdp file and I get a smaller value of particles in the message error, but still a crash. The box size has also no effect on the message error. I have checked the starting structure and everything is fine. Mutating that Asn to a non-charged residue does not yield any problem, but I want to study the effect in the Asn-- Lys mutation. Any hint to solve the error? If EM stops at the first step, there's usually something catastrophically wrong with the starting configuration. If you've decreased the value of emstep, there's little else that will account for such behavior. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Difference in Number of contacts through g_hbond and g_mindist
On 3/4/13 9:08 AM, bipin singh wrote: Hi All, I have a doubt regarding the calculation of number of contacts between two groups. Because, I am getting different number of contacts calculated through g_hbond -contact option and g_mindist -on option. I have used same cutoff for distance (0.6nm) in both the cases. How different are the results? The g_hbond code is very complex, but you'd probably have to go into the inner workings of both programs to understand why. I also do not know whether other settings in g_hbond will matter, like -merge, or whether or not g_hbond will only calculate contacts among H-bond participating groups. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Protein-ligand simulation
On 3/4/13 9:15 AM, Ankita naithani wrote: Hi, I recently ran a simulation with the complete structure of my protein alongwith the ligands. I was running some analysis and was trying out the Principal component analysis. I used the g_covar tool to get the eigenvalues and eigenvectors for protein back bone. However, when I try to use g_covar for the whole system, it shows me segmentation fault. My problem is that I want to see the simulation of my protein and ligand together as a whole. I ran g_covar individually for all the ligands and saw the first eigenvector movie in pymol and similarly for protein backbone. But I would really like to see the ligand and protein dynamics together because when I see the eigenvector individually, the ligand is moving in a direction probably towards the binding site and it would be quite helpful if anyone could suggest how can I possibly view them together. Like any Gromacs tool, you can create an index group of whatever subset of atoms you would like to consider. The segmentation fault when considering the whole system likely resulted in an exhaustion of available memory, which is not surprising given the size of the matrix. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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
[gmx-users] Re: Output for rmsd and radius of gyration doubts
Hi Justin, I tried running the simulation for 10ns and this time, my RMSD graph shows a stable fluctuation of 0.45nm from 2.5ns to 10ns. The radius of gyration shows stable fluctuation from 4ns to 10ns around 2.46nm. My doubt is, shouldn't the RMSD be fluctuating at 0.1nm? Does it mean that my structure is not stable? Or do I need to run more than 10ns of simulation? Please advice. :( I attached a screenshot of the graph in case I didn't explain it well. g_rms http://postimage.org/image/f4bkobtx9/ g_gyrate http://postimage.org/image/gd86i2jpj/ Thanking you in advance. Best wishes -- View this message in context: http://gromacs.5086.n6.nabble.com/Output-for-rmsd-and-radius-of-gyration-doubts-tp5005881p5006080.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: Output for rmsd and radius of gyration doubts
On 3/4/13 9:49 AM, Ewaru wrote: Hi Justin, I tried running the simulation for 10ns and this time, my RMSD graph shows a stable fluctuation of 0.45nm from 2.5ns to 10ns. The radius of gyration shows stable fluctuation from 4ns to 10ns around 2.46nm. My doubt is, shouldn't the RMSD be fluctuating at 0.1nm? Does it mean that my structure is not stable? Or do I need to run more than 10ns of simulation? Why would you assume that your RMSD would be 0.1 nm? That's quite low, even for the most stable of proteins. Please advice. :( I attached a screenshot of the graph in case I didn't explain it well. g_rms http://postimage.org/image/f4bkobtx9/ g_gyrate http://postimage.org/image/gd86i2jpj/ Protein properties fluctuate over time, and can correspond to behaviors that are both subtle and obvious. Small changes in secondary structure can account for fluctuations in RMSD, larger domain motions or loop regions flopping around would explain larger spikes in RMSD or Rg. I don't know what system you're working with or what your goals are, but in general, 10 ns is still considered very short for all but the fastest motions in proteins. Domain motions and other tertiary movements may take anywhere from tens or hundreds of nanoseconds to the microsecond time frame. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Difference in Number of contacts through g_hbond and g_mindist
Thanks for the reply. The difference is almost double, through g_hbond the average number of contacts are 1821 and through g_mindist it is 3643. The calculation group does not contains hydrogen atoms. On Mon, Mar 4, 2013 at 8:14 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 9:08 AM, bipin singh wrote: Hi All, I have a doubt regarding the calculation of number of contacts between two groups. Because, I am getting different number of contacts calculated through g_hbond -contact option and g_mindist -on option. I have used same cutoff for distance (0.6nm) in both the cases. How different are the results? The g_hbond code is very complex, but you'd probably have to go into the inner workings of both programs to understand why. I also do not know whether other settings in g_hbond will matter, like -merge, or whether or not g_hbond will only calculate contacts among H-bond participating groups. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- 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] Difference in Number of contacts through g_hbond and g_mindist
As Justin implied, -merge could potentially make a factor of 2. Try g_hbond -nomerge. Erik On Mar 4, 2013, at 4:02 PM, bipin singh wrote: Thanks for the reply. The difference is almost double, through g_hbond the average number of contacts are 1821 and through g_mindist it is 3643. The calculation group does not contains hydrogen atoms. On Mon, Mar 4, 2013 at 8:14 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 9:08 AM, bipin singh wrote: Hi All, I have a doubt regarding the calculation of number of contacts between two groups. Because, I am getting different number of contacts calculated through g_hbond -contact option and g_mindist -on option. I have used same cutoff for distance (0.6nm) in both the cases. How different are the results? The g_hbond code is very complex, but you'd probably have to go into the inner workings of both programs to understand why. I also do not know whether other settings in g_hbond will matter, like -merge, or whether or not g_hbond will only calculate contacts among H-bond participating groups. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- 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 -- 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
[gmx-users] Re: Output for rmsd and radius of gyration doubts
Hi Justin, Thank you for your prompt reply! As this is my first approach to molecular dynamics, I still have lots of to understand but I'm constantly reading and trying to work things out. I predicted 2 structures, one using Modeller, and another one with I-Tasser. I followed your very informative tutorial for the approach of energy minimization and equilibration using Gromacs. My mistake for assuming that RMSD should fall within 0.1nm. I'm supposed to choose the best model to proceed with docking. Is it okay if I run just a 10ns simulation for both the predicted structure and then decide the best one by comparing the stability of the protein, from the output of the RMSD and radius of gyration? Thank you in advance. Best wishes -- View this message in context: http://gromacs.5086.n6.nabble.com/Output-for-rmsd-and-radius-of-gyration-doubts-tp5005881p5006085.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: Output for rmsd and radius of gyration doubts
On 3/4/13 10:37 AM, Ewaru wrote: Hi Justin, Thank you for your prompt reply! As this is my first approach to molecular dynamics, I still have lots of to understand but I'm constantly reading and trying to work things out. I predicted 2 structures, one using Modeller, and another one with I-Tasser. I followed your very informative tutorial for the approach of energy minimization and equilibration using Gromacs. My mistake for assuming that RMSD should fall within 0.1nm. I'm supposed to choose the best model to proceed with docking. Is it okay if I run just a 10ns simulation for both the predicted structure and then decide the best one by comparing the stability of the protein, from the output of the RMSD and radius of gyration? Radius of gyration is probably not the best criterion here; I just demonstrated it in the tutorial because it is a rather fool-proof program. RMSD is a decent indicator of structural changes, but by itself doesn't necessarily indicate convergence or tell you anything useful about the structure. You need to apply some real biological knowledge before concluding which model is best. Since successful docking requires an accurate representation of the binding site, you need to probably examine the stability of critical residues, interactions among them, etc. There are far more metrics that can be assessed than just trivial things like RMSD and Rg. The tutorial is by no means comprehensive (nor does it claim to be), so spending some time in the literature and reading textbooks about these techniques should be prerequisite. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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
[gmx-users] Re: Output for rmsd and radius of gyration doubts
Thank you so much, Justin! Yes, I will do so. :) Take care. Best wishes. -- View this message in context: http://gromacs.5086.n6.nabble.com/Output-for-rmsd-and-radius-of-gyration-doubts-tp5005881p5006087.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] about simulation runs
On 3/4/13 11:20 AM, amna khan wrote: hi, i want to ask i have i3 laptop i want to run the 1ns simulations how much time it will take ? There is no way to tell. The time it takes depends on the size of the system (number of atoms) and algorithms chosen. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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
[gmx-users] g_hbond and contact
Dear users, I used the following tool for finding the contacts g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx -num a.xvg From the index file, the number of contacts of each atom was extracted. This and the xvg output was compared with another simulation. It was found that the number of contacts was more in 2nd simulation compared to the first. But When I compared xvg file it was showing the opposite behaviour. The contacts was also calculated using g_mdmat for the same cutoff and it was agreeing with the numbers I got from in index output of g_hbond. Why is this difference in index and xvg output? Also the xvg file looks like - s0 legend Contacts @ s1 legend Pairs within 0.4 nm 40007496 0 40027513 0 40047605 0 40067531 0 40087573 0 40107546 0 40127544 0 40147526 0 40167530 0 40187496 0 40207526 0 .. Thank you kavya -- 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] g_hbond and contact
On 3/4/13 11:25 AM, Kavyashree M wrote: Dear users, I used the following tool for finding the contacts g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx -num a.xvg From the index file, the number of contacts of each atom was extracted. This and the xvg output was compared with another simulation. It was found that the number of contacts was more in 2nd simulation compared to the first. But When I compared xvg file it was showing the opposite behaviour. These statements don't make any sense. How did you determine that the number of contacts in simulation 2 was greater than simulation 1, but then the .xvg files showed the opposite? The number of contacts come from the .xvg files? Perhaps you simply swapped your files during analysis. The contacts was also calculated using g_mdmat for the same cutoff and it was agreeing with the numbers I got from in index output of g_hbond. Why is this difference in index and xvg output? An index group is a list of atom numbers. The .xvg output is whatever you tell it to be, in this case, the number of contacts within the group selected. -Justin Also the xvg file looks like - s0 legend Contacts @ s1 legend Pairs within 0.4 nm 40007496 0 40027513 0 40047605 0 40067531 0 40087573 0 40107546 0 40127544 0 40147526 0 40167530 0 40187496 0 40207526 0 .. Thank you kavya -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Difference in Number of contacts through g_hbond and g_mindist
Thanks a lot for the suggestions. It worked. On Mon, Mar 4, 2013 at 8:44 PM, Erik Marklund er...@xray.bmc.uu.se wrote: As Justin implied, -merge could potentially make a factor of 2. Try g_hbond -nomerge. Erik On Mar 4, 2013, at 4:02 PM, bipin singh wrote: Thanks for the reply. The difference is almost double, through g_hbond the average number of contacts are 1821 and through g_mindist it is 3643. The calculation group does not contains hydrogen atoms. On Mon, Mar 4, 2013 at 8:14 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 9:08 AM, bipin singh wrote: Hi All, I have a doubt regarding the calculation of number of contacts between two groups. Because, I am getting different number of contacts calculated through g_hbond -contact option and g_mindist -on option. I have used same cutoff for distance (0.6nm) in both the cases. How different are the results? The g_hbond code is very complex, but you'd probably have to go into the inner workings of both programs to understand why. I also do not know whether other settings in g_hbond will matter, like -merge, or whether or not g_hbond will only calculate contacts among H-bond participating groups. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- 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] g_hbond and contact
Sir, From Index file which gives the unique contacts - First section the list of atoms I want to analyse [ C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ] second section : the unique contacts of each atoms with others [ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5292 5296 530 From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 Total/mean @ legend string 1 Total @ legend string 2 Mean @ legend string 3 # atoms @ legend string 4 Mean/# atoms #resratio tot mean natm mean/atm 1 1.001 1110.991110.991 2 1.244 10 8.0411 8.041 3 1.166 1311.147111.147 4 1.036 1110.615110.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. I hope I am clear this time. Thank you kavya On Mon, Mar 4, 2013 at 10:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 11:25 AM, Kavyashree M wrote: Dear users, I used the following tool for finding the contacts g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx -num a.xvg From the index file, the number of contacts of each atom was extracted. This and the xvg output was compared with another simulation. It was found that the number of contacts was more in 2nd simulation compared to the first. But When I compared xvg file it was showing the opposite behaviour. These statements don't make any sense. How did you determine that the number of contacts in simulation 2 was greater than simulation 1, but then the .xvg files showed the opposite? The number of contacts come from the .xvg files? Perhaps you simply swapped your files during analysis. The contacts was also calculated using g_mdmat for the same cutoff and it was agreeing with the numbers I got from in index output of g_hbond. Why is this difference in index and xvg output? An index group is a list of atom numbers. The .xvg output is whatever you tell it to be, in this case, the number of contacts within the group selected. -Justin Also the xvg file looks like - s0 legend Contacts @ s1 legend Pairs within 0.4 nm 40007496 0 40027513 0 40047605 0 40067531 0 40087573 0 40107546 0 40127544 0 40147526 0 40167530 0 40187496 0 40207526 0 .. Thank you kavya -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] about simulation runs
2230 atoms and same as tutorial On Mon, Mar 4, 2013 at 9:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 11:20 AM, amna khan wrote: hi, i want to ask i have i3 laptop i want to run the 1ns simulations how much time it will take ? There is no way to tell. The time it takes depends on the size of the system (number of atoms) and algorithms chosen. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] about simulation runs
and what about gromacs webserver ? can i submit all my prepared files there ? On Mon, Mar 4, 2013 at 10:27 PM, amna khan amnakhan...@gmail.com wrote: 2230 atoms and same as tutorial On Mon, Mar 4, 2013 at 9:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 11:20 AM, amna khan wrote: hi, i want to ask i have i3 laptop i want to run the 1ns simulations how much time it will take ? There is no way to tell. The time it takes depends on the size of the system (number of atoms) and algorithms chosen. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] g_hbond and contact
On 3/4/13 12:04 PM, Kavyashree M wrote: Sir, From Index file which gives the unique contacts - First section the list of atoms I want to analyse When measuring contacts, you don't measure one group, you measure the number of contacts that occur between groups A and B, which considers all atoms in those two groups. [ C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ] second section : the unique contacts of each atoms with others You don't define contacts in an index group, you define atoms that may or may not make contacts with others. [ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5292 5296 530 There's something very wrong with this index file. How did you generate it? The presence of a repeated atom number (5) and a nonsensical one (7ws) leads me to believe that you've done something incorrect. Did this come from g_hbond? It looks like the output of -hbn, which is only useful for decoding hbmap.xpm, nothing else. From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 Total/mean @ legend string 1 Total @ legend string 2 Mean @ legend string 3 # atoms @ legend string 4 Mean/# atoms #resratio tot mean natm mean/atm 1 1.001 1110.991110.991 2 1.244 10 8.0411 8.041 3 1.166 1311.147111.147 4 1.036 1110.615110.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. That shouldn't be unexpected. Two independent simulations have no guarantee of doing the same thing, that's why sampling is so important. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] about simulation runs
On 3/4/13 12:27 PM, amna khan wrote: 2230 atoms and same as tutorial I'm assuming that you are using implicit solvent then? Which tutorial are you referring to? -Justin On Mon, Mar 4, 2013 at 9:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 11:20 AM, amna khan wrote: hi, i want to ask i have i3 laptop i want to run the 1ns simulations how much time it will take ? There is no way to tell. The time it takes depends on the size of the system (number of atoms) and algorithms chosen. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist 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/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
[gmx-users] Re: ERROR No default G96Angle types
I added this line (CA C Oga_30) to topology file and problem solved. Justin are right as usual, Regards, Eduardo. - Eduardo Villarreal Ramírez Postdoctoral Research Fellow Mineralized Tissue Laboratory, Hospital for Special Surgery. -- View this message in context: http://gromacs.5086.n6.nabble.com/ERROR-No-default-G96Angle-types-tp5006044p5006099.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] g_hbond and contact
On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote: When measuring contacts, you don't measure one group, you measure the number of contacts that occur between groups A and B, which considers all atoms in those two groups. I gave a group of hydrophobic atoms in both cases The command I gave - g_hbond_46 -fx.xtc-s x.tpr-contact -n x.ndx -r 0.4 -hbm o.xpm -hbn o.ndx -num o.xvg my index file contained a group of hydrophobic atoms. which I supplied in the x.ndx. You don't define contacts in an index group, you define atoms that may or may not make contacts with others. The one I mentioned here is the output index file from the g_hbond (4.6 version) - o.ndx. [ contacts_C_CA_CB_CD_CD1_CD2_**CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_**CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5292 5296 530 There's something very wrong with this index file. How did you generate it? The presence of a repeated atom number (5) and a nonsensical one (7ws) leads me to believe that you've done something incorrect. Did this come from g_hbond? It looks like the output of -hbn, which is only useful for decoding hbmap.xpm, nothing else. I did not generate this. The tool (g_hbond) generated this index file. It is the -hbn output. From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 Total/mean @ legend string 1 Total @ legend string 2 Mean @ legend string 3 # atoms @ legend string 4 Mean/# atoms #resratio tot mean natm mean/atm 1 1.001 1110.991110.991 2 1.244 10 8.0411 8.041 3 1.166 1311.147111.147 4 1.036 1110.615110.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. That shouldn't be unexpected. Two independent simulations have no guarantee of doing the same thing, that's why sampling is so important. Thank you kavya -- 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] g_hbond and contact
On 3/4/13 1:10 PM, Kavyashree M wrote: On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote: When measuring contacts, you don't measure one group, you measure the number of contacts that occur between groups A and B, which considers all atoms in those two groups. I gave a group of hydrophobic atoms in both cases The command I gave - g_hbond_46 -fx.xtc-s x.tpr-contact -n x.ndx -r 0.4 -hbm o.xpm -hbn o.ndx -num o.xvg my index file contained a group of hydrophobic atoms. which I supplied in the x.ndx. You don't define contacts in an index group, you define atoms that may or may not make contacts with others. The one I mentioned here is the output index file from the g_hbond (4.6 version) - o.ndx. [ contacts_C_CA_CB_CD_CD1_CD2_**CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_**CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5292 5296 530 There's something very wrong with this index file. How did you generate it? The presence of a repeated atom number (5) and a nonsensical one (7ws) leads me to believe that you've done something incorrect. Did this come from g_hbond? It looks like the output of -hbn, which is only useful for decoding hbmap.xpm, nothing else. I did not generate this. The tool (g_hbond) generated this index file. It is the -hbn output. OK, then I still don't know what 7ws is, but the only purpose for this file is to provide a key to the existence matrix in hbmap.xpm. Your previous description indicated that you were using it for some other analysis, which would not be appropriate. The other thing worth mentioning here is something that was posted to the list just a few hours ago, that the output of g_hbond -contact may not agree with other methods of calculating contacts, especially in the case of -merge vs. -nomerge. -Justin From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 Total/mean @ legend string 1 Total @ legend string 2 Mean @ legend string 3 # atoms @ legend string 4 Mean/# atoms #resratio tot mean natm mean/atm 1 1.001 1110.991110.991 2 1.244 10 8.0411 8.041 3 1.166 1311.147111.147 4 1.036 1110.615110.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. That shouldn't be unexpected. Two independent simulations have no guarantee of doing the same thing, that's why sampling is so important. Thank you kavya -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Re: gInstallation Problems with Gromacs4.6
OK, but that still might not be fixing the real problem, which might be
starting with how you are calling cmake in the first place.
Mark
Actually, i called the cmake-2.8.10 which i had installed in my home
directory as the one installed on the cluster was an old version.
so i cd to the cmake-build directory and gave the full path to the cmake
executable.
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake ..
I don't understand how this could have caused any installation problem.
Before this i also tried to use the older version cmake installed on the
cluster but that also gave me the same error.
In any case, gromacs4.6 got installed properly by disabling shared
libraries and is up and running. Though i would be interested in knowing
if its possible to remove this error in any other way.
with regards
Abhishek
On Sat, Mar 2, 2013 at 7:20 AM, Abhishek Acharya
aacha...@iitk.ac.inwrote:
Date: Fri, 1 Mar 2013 23:59:36 +0530
From: Abhishek Acharya aacha...@iitk.ac.in
Subject: [gmx-users] Installation Problems with Gromacs4.6
To: gromacs maillist gmx-users@gromacs.org
Message-ID:
2ca7063e41d6ddfa7ea411dc3cfe3ad3.squir...@webmail.iitk.ac.in
Content-Type: text/plain;charset=iso-8859-1
Hello Gromacs Users.
I have been trying to install Gromacs4.6 on our HPC facility. I think
I
have correctly provided all the necessary mpi and fftw library paths.
But
when i try to run configure it gives me the following error:
CMake Error at cmake/FindFFTW.cmake:105 (message):
Could not find fftwf_plan_r2r_1d in
/home/aacharya/softwares/fftw-3.3.3/lib/libfftw3f.so, take a look
at
the
error message in
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeError.log
to
find out what went wrong. If you are using a static lib (.a) make
sure
you
have specified all dependencies of fftw3f in FFTWF_LIBRARY by hand
(e.g.
-DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):
CMakeLists.txt:894 (find_package)
As suggested here I looked into the CMakeError.log file of which I
can't
make any sense.
Source file was:
#include mpi.h
int main(void) {
void* buf;
MPI_Allreduce(MPI_IN_PLACE, buf, 10, MPI_FLOAT, MPI_SUM,
MPI_COMM_WORLD);
}
Determining if the function fftwf_plan_r2r_1d exists in the
/home/aacharya/softwares/fftw-3.3.3/lib failed with the following
output:
Change Dir:
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/gmake cmTryCompileExec2668319475/fast
/usr/bin/gmake -f
CMakeFiles/cmTryCompileExec2668319475.dir/build.make
CMakeFiles/cmTryCompileExec2668319475.dir/build
gmake[1]: Entering directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E
cmake_progress_report
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp/CMakeFiles
1
Building C object
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
/usr/bin/cc -Wextra -Wno-missing-field-initializers
-Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d -o
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
-c
/home/aacharya/softwares/cmake-2.8.10.2/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec2668319475
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E
cmake_link_script
CMakeFiles/cmTryCompileExec2668319475.dir/link.txt --verbose=1
/usr/bin/cc -Wextra -Wno-missing-field-initializers
-Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d
-L/home/aacharya/softwares/fftw-3.3.3/lib
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -o
cmTryCompileExec2668319475 -rdynamic -lm
Strange, there is supposed to be a -lfftw3f before -lm. Can you
tell us what your cmake command line was?
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o: In
function `main':
CheckFunctionExists.c:(.text+0x15): undefined reference to
`fftwf_plan_r2r_1d'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTryCompileExec2668319475] Error 1
gmake[1]: Leaving directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec2668319475/fast] Error 2
Kindly help. I tried installing 4.5.6 and it got installed without
any
such problems. I need 4.6 because my tpr files are produced in
Gromacs4.6
and I am using the Verlet cutoff scheme.
Thank you Mark and Christoph for your replies. I solved the installation
problem by configuring gromacs with static libraries. I somehow didn't
notice earlier, there was a note saying that Shared Libraries might be
problematic with MPI.
With Regards
Abhishek
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the
Re: [gmx-users] X particles communicated to PME node Y are more ...
I have tried the same issue (same system with same mdp file and same initial configuration as starting structure) and is running without any problems with GROMACS-4.5.5. Anyone knows what is happening? 2013/3/4, Justin Lemkul jalem...@vt.edu: On 3/4/13 8:25 AM, Miguel Ángel Mompeán García wrote: Dear gmx users, I have successfully performed simulations on a charged peptide. I did a series of mutations and everything had a happy end. Now I have tried another mutation (just substitution of Asn to Lys) and I am getting the well-known X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group message error during energy minimization, right at the beginning (step 0). My energy minimization mdp file looks as follows: integrator = steep ; emtol = 1000.0; emstep = 0.02 ; nsteps = 7 ; nstlist = 1 ; ns_type = grid; rlist = 1.0 ; coulombtype = PME ; rcoulomb= 1.0; rvdw= 1.0 ; pbc = xyz; I have tried without neutralizing with ions, changing the time step, changing the integrator and the values for rcoulomb,rlist, etc. Bad idea. Nonbonded cutoffs are an intrinsic part of the force field. Changing them will actually increase your likelihood of failure. I have changed all the parameteres in the mdp file and I get a smaller value of particles in the message error, but still a crash. The box size has also no effect on the message error. I have checked the starting structure and everything is fine. Mutating that Asn to a non-charged residue does not yield any problem, but I want to study the effect in the Asn-- Lys mutation. Any hint to solve the error? If EM stops at the first step, there's usually something catastrophically wrong with the starting configuration. If you've decreased the value of emstep, there's little else that will account for such behavior. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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 -- 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] X particles communicated to PME node Y are more ...
On 3/4/13 3:08 PM, Miguel Ángel Mompeán García wrote: I have tried the same issue (same system with same mdp file and same initial configuration as starting structure) and is running without any problems with GROMACS-4.5.5. Anyone knows what is happening? You didn't tell us your Gromacs version in the previous post so the best guess is random bug that was somehow fixed before 4.5.5. -Justin 2013/3/4, Justin Lemkul jalem...@vt.edu: On 3/4/13 8:25 AM, Miguel Ángel Mompeán García wrote: Dear gmx users, I have successfully performed simulations on a charged peptide. I did a series of mutations and everything had a happy end. Now I have tried another mutation (just substitution of Asn to Lys) and I am getting the well-known X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group message error during energy minimization, right at the beginning (step 0). My energy minimization mdp file looks as follows: integrator = steep ; emtol = 1000.0; emstep = 0.02 ; nsteps = 7 ; nstlist = 1 ; ns_type = grid; rlist = 1.0 ; coulombtype = PME ; rcoulomb= 1.0; rvdw= 1.0 ; pbc = xyz; I have tried without neutralizing with ions, changing the time step, changing the integrator and the values for rcoulomb,rlist, etc. Bad idea. Nonbonded cutoffs are an intrinsic part of the force field. Changing them will actually increase your likelihood of failure. I have changed all the parameteres in the mdp file and I get a smaller value of particles in the message error, but still a crash. The box size has also no effect on the message error. I have checked the starting structure and everything is fine. Mutating that Asn to a non-charged residue does not yield any problem, but I want to study the effect in the Asn-- Lys mutation. Any hint to solve the error? If EM stops at the first step, there's usually something catastrophically wrong with the starting configuration. If you've decreased the value of emstep, there's little else that will account for such behavior. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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 -- Justin A. Lemkul, Ph.D. Research Scientist 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/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] Thread affinity setting failed
Hi, There are some clarifications needed and as this might help you and other understand what's going on, I'll take the time to explain things. Affinity setting is a low-, operating system-level, operation and locks (=pins) threads to physical cores of the CPU preventing the OS from moving them which can cause performance drop - especially when using OpenMP-multithreading on multi-socket and NUMA machines. Now, mdrun will by default *try* to set affinity if you use all cores detected (i.e if mdrun can be sure that it is the only application running on the machine), but will by default *not* set thread affinities if the number of thread/processes per compute node is less than the number of cores detected. Hence, when you decrease -ntmpi to 7, you implicitly end up turning off thread pinning, that's why the warnings don't show up. The fact that affinity setting fails on your machine suggests that either the system libraries don't support this or the mdrun code is not fully compatible with your OS, the type of CPUs AFAIK don't matter at all. What OS are you using? Is it an old installation? If you are not using OpenMP - which btw you probably should with the Verlet scheme if you are running running on a single node or at high parallelization -, the performance will not be affected very much by the lack of thread pinning. While the warnings themselves can often be safely ignored, if only some of the threads/processes can't set affinities, this might indicate a problem. I your case, if you were really seeing only 5 cores being used with 3 warnings, this might suggest that while the affinity setting failed, three threads are using already busy cores overlapping with others which will cause severe performance drop. What you can do to avoid the performance drop is to turn of pinning by passing -pin off to mdrun. Without OpenMP this will typically not cause a large performance drop compared to having correct pinning and it will avoid the bad overlapping threads/processes case. I suspect that your machines might be running an old OS which could be causing the failed affinity setting. If that is the case, you should talk to your sysadmins and have them figure out the issue. If you have a moderately new OS, you should not be seeing such issues, so I suggest that you file a bug report with details like: OS + version + kernel version, pthread library version, standard C library version. Cheers, -- Szilárd On Mon, Mar 4, 2013 at 1:45 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Mon, Mar 4, 2013 at 6:02 AM, Reid Van Lehn rvanl...@mit.edu wrote: Hello users, I ran into a bug I do not understand today upon upgrading from v. 4.5.5 to v 4.6. I'm using older 8 core Intel Xeon E5430 machines, and when I submitted a job for 8 cores to one of the nodes I received the following error: NOTE: In thread-MPI thread #3: Affinity setting failed. This can cause performance degradation! NOTE: In thread-MPI thread #2: Affinity setting failed. This can cause performance degradation! NOTE: In thread-MPI thread #1: Affinity setting failed. This can cause performance degradation! I ran mdrun simply with the flags: mdrun -v -ntmpi 8 -deffnm em Using the top command, I confirmed that no other programs were running and that mdrun was in fact only using 5 cores. Reducing -ntmpi to 7, however, resulted in no error (only a warning about not using all of the logical cores) and mdrun used 7 cores correctly. Since it warned about thread affinity settings, I tried setting -pin on -pinoffset 0 even though I was using all the cores on the machine. This resulted in the same error. However, turning pinning off explicitly with -pin off (rather than -pin auto) did correctly give me the all 8 cores again. While I figured out a solution in this particular instance, my question is whether I should be have known from my hardware/settings that pinning should be turned off (for future reference), or if this is a bug? I'm not sure - those are 2007-era processors, so there may be some limitations in what they could do (or how well the kernel and system libraries support it). So investing time into working out the real problem is not really worthwhile. Thanks for reporting your work-around, however, others might benefit from it. If you plan on doing lengthy simulations, you might like to verify that you get linear scaling with increasing -ntmpi, and/or compare performance with the MPI version on the same hardware. 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 -- gmx-users mailing list
Re: [gmx-users] X particles communicated to PME node Y are more ...
The version I was using this morning was 4.6 2013/3/4, Justin Lemkul jalem...@vt.edu: On 3/4/13 3:08 PM, Miguel Ángel Mompeán García wrote: I have tried the same issue (same system with same mdp file and same initial configuration as starting structure) and is running without any problems with GROMACS-4.5.5. Anyone knows what is happening? You didn't tell us your Gromacs version in the previous post so the best guess is random bug that was somehow fixed before 4.5.5. -Justin 2013/3/4, Justin Lemkul jalem...@vt.edu: On 3/4/13 8:25 AM, Miguel Ángel Mompeán García wrote: Dear gmx users, I have successfully performed simulations on a charged peptide. I did a series of mutations and everything had a happy end. Now I have tried another mutation (just substitution of Asn to Lys) and I am getting the well-known X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group message error during energy minimization, right at the beginning (step 0). My energy minimization mdp file looks as follows: integrator = steep ; emtol = 1000.0; emstep = 0.02 ; nsteps = 7 ; nstlist = 1 ; ns_type = grid; rlist = 1.0 ; coulombtype = PME ; rcoulomb= 1.0; rvdw= 1.0 ; pbc = xyz; I have tried without neutralizing with ions, changing the time step, changing the integrator and the values for rcoulomb,rlist, etc. Bad idea. Nonbonded cutoffs are an intrinsic part of the force field. Changing them will actually increase your likelihood of failure. I have changed all the parameteres in the mdp file and I get a smaller value of particles in the message error, but still a crash. The box size has also no effect on the message error. I have checked the starting structure and everything is fine. Mutating that Asn to a non-charged residue does not yield any problem, but I want to study the effect in the Asn-- Lys mutation. Any hint to solve the error? If EM stops at the first step, there's usually something catastrophically wrong with the starting configuration. If you've decreased the value of emstep, there's little else that will account for such behavior. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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 -- Justin A. Lemkul, Ph.D. Research Scientist 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/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 -- 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] X particles communicated to PME node Y are more ...
On 3/4/13 4:11 PM, Miguel Ángel Mompeán García wrote: The version I was using this morning was 4.6 In that case, it's probably something worth pursuing. Having the new version fail when an older version works is curious. Can you please provide all of the following details: 1. Compilers used to build Gromacs 2. Hardware description 3. mdrun command 4. Complete .mdp file -Justin 2013/3/4, Justin Lemkul jalem...@vt.edu: On 3/4/13 3:08 PM, Miguel Ángel Mompeán García wrote: I have tried the same issue (same system with same mdp file and same initial configuration as starting structure) and is running without any problems with GROMACS-4.5.5. Anyone knows what is happening? You didn't tell us your Gromacs version in the previous post so the best guess is random bug that was somehow fixed before 4.5.5. -Justin 2013/3/4, Justin Lemkul jalem...@vt.edu: On 3/4/13 8:25 AM, Miguel Ángel Mompeán García wrote: Dear gmx users, I have successfully performed simulations on a charged peptide. I did a series of mutations and everything had a happy end. Now I have tried another mutation (just substitution of Asn to Lys) and I am getting the well-known X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group message error during energy minimization, right at the beginning (step 0). My energy minimization mdp file looks as follows: integrator = steep ; emtol = 1000.0; emstep = 0.02 ; nsteps = 7 ; nstlist = 1 ; ns_type = grid; rlist = 1.0 ; coulombtype = PME ; rcoulomb= 1.0; rvdw= 1.0 ; pbc = xyz; I have tried without neutralizing with ions, changing the time step, changing the integrator and the values for rcoulomb,rlist, etc. Bad idea. Nonbonded cutoffs are an intrinsic part of the force field. Changing them will actually increase your likelihood of failure. I have changed all the parameteres in the mdp file and I get a smaller value of particles in the message error, but still a crash. The box size has also no effect on the message error. I have checked the starting structure and everything is fine. Mutating that Asn to a non-charged residue does not yield any problem, but I want to study the effect in the Asn-- Lys mutation. Any hint to solve the error? If EM stops at the first step, there's usually something catastrophically wrong with the starting configuration. If you've decreased the value of emstep, there's little else that will account for such behavior. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/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 -- Justin A. Lemkul, Ph.D. Research Scientist 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/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 -- Justin A. Lemkul, Ph.D. Research Scientist 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/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
[gmx-users] Time-Dependent Electric Field
Gromacs users, I am trying to run a simulation with a time dependent electric field with frequency of around 16 GHz in the Z direction. What numbers should I put in the .mdp file following E-zt: for a field with this frequency? I have looked at the source code but cannot determine what units the frequency should be in. Currently, for electric Field I have the following: E-z = 1 .5 1 E-zt= 1 (some number) 0 I want to know what the some number should look like. Any help is appreciated. Regards, Ross Quick -- View this message in context: http://gromacs.5086.n6.nabble.com/Time-Dependent-Electric-Field-tp5006108.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: gInstallation Problems with Gromacs4.6
By asking how you calling cmake I mean that cmake takes a number of
command-line options, and since using those inappropriately (or not calling
the right MPI wrapper compiler) might cause symptoms like yours, we need
more complete information to have a chance of helping solve your problem.
Christoph also asked for your cmake command line.
Mark
On Mon, Mar 4, 2013 at 9:04 PM, Abhishek Acharya aacha...@iitk.ac.inwrote:
OK, but that still might not be fixing the real problem, which might be
starting with how you are calling cmake in the first place.
Mark
Actually, i called the cmake-2.8.10 which i had installed in my home
directory as the one installed on the cluster was an old version.
so i cd to the cmake-build directory and gave the full path to the cmake
executable.
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake ..
I don't understand how this could have caused any installation problem.
Before this i also tried to use the older version cmake installed on the
cluster but that also gave me the same error.
In any case, gromacs4.6 got installed properly by disabling shared
libraries and is up and running. Though i would be interested in knowing
if its possible to remove this error in any other way.
with regards
Abhishek
On Sat, Mar 2, 2013 at 7:20 AM, Abhishek Acharya
aacha...@iitk.ac.inwrote:
Date: Fri, 1 Mar 2013 23:59:36 +0530
From: Abhishek Acharya aacha...@iitk.ac.in
Subject: [gmx-users] Installation Problems with Gromacs4.6
To: gromacs maillist gmx-users@gromacs.org
Message-ID:
2ca7063e41d6ddfa7ea411dc3cfe3ad3.squir...@webmail.iitk.ac.in
Content-Type: text/plain;charset=iso-8859-1
Hello Gromacs Users.
I have been trying to install Gromacs4.6 on our HPC facility. I think
I
have correctly provided all the necessary mpi and fftw library paths.
But
when i try to run configure it gives me the following error:
CMake Error at cmake/FindFFTW.cmake:105 (message):
Could not find fftwf_plan_r2r_1d in
/home/aacharya/softwares/fftw-3.3.3/lib/libfftw3f.so, take a look
at
the
error message in
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeError.log
to
find out what went wrong. If you are using a static lib (.a) make
sure
you
have specified all dependencies of fftw3f in FFTWF_LIBRARY by hand
(e.g.
-DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):
CMakeLists.txt:894 (find_package)
As suggested here I looked into the CMakeError.log file of which I
can't
make any sense.
Source file was:
#include mpi.h
int main(void) {
void* buf;
MPI_Allreduce(MPI_IN_PLACE, buf, 10, MPI_FLOAT, MPI_SUM,
MPI_COMM_WORLD);
}
Determining if the function fftwf_plan_r2r_1d exists in the
/home/aacharya/softwares/fftw-3.3.3/lib failed with the following
output:
Change Dir:
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/gmake cmTryCompileExec2668319475/fast
/usr/bin/gmake -f
CMakeFiles/cmTryCompileExec2668319475.dir/build.make
CMakeFiles/cmTryCompileExec2668319475.dir/build
gmake[1]: Entering directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E
cmake_progress_report
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp/CMakeFiles
1
Building C object
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
/usr/bin/cc -Wextra -Wno-missing-field-initializers
-Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d -o
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
-c
/home/aacharya/softwares/cmake-2.8.10.2/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec2668319475
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E
cmake_link_script
CMakeFiles/cmTryCompileExec2668319475.dir/link.txt --verbose=1
/usr/bin/cc -Wextra -Wno-missing-field-initializers
-Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d
-L/home/aacharya/softwares/fftw-3.3.3/lib
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -o
cmTryCompileExec2668319475 -rdynamic -lm
Strange, there is supposed to be a -lfftw3f before -lm. Can you
tell us what your cmake command line was?
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o: In
function `main':
CheckFunctionExists.c:(.text+0x15): undefined reference to
`fftwf_plan_r2r_1d'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTryCompileExec2668319475] Error 1
gmake[1]: Leaving directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec2668319475/fast] Error 2
Kindly help. I tried installing 4.5.6 and it got
Re: [gmx-users] Shifting in Verlet cut-off schemes?
On Sat, Mar 2, 2013 at 6:40 PM, Yun Shi yunsh...@gmail.com wrote: Hi all, I have read http://www.gromacs.org/Documentation/Cut-off_schemes, but still unsure about how Verlet works. The group cut-off scheme can be combined with a buffered pair-list..The Verlet list scheme has buffered neighborlists with exact cut-off's. What does buffered neighborlists mean? Including neighbors beyond the cutoff distance (e.g. 1.0 nm)? Then what is the delta-distance for this buffer region? See manual 7.3.9 LJ and Coulomb potential are by default shifted to zero by subtracting the value at the cut-off. Does the program only do such subtractions at exactly the cutoff distance? Or does it shift both potential functions throughout the entire distance range (e.g. from 0 to 1.0 nm)? The latter. Doing it at the cut-off would serve no purpose at all (since it is zero after the cut-off, by definition). Then would this cause potential problems since some force fields are not parametrized with a shifting approach? In principle, yes. Many force fields were parameterized using methods that are either now totally unused, or that remain in favour pretty much because of those force fields :-) As always in computational chemistry, you need to seek a method reasonably likely to lead to an accurate model of reality. Combing the literature for the necessary insight is difficult, but unless someone has already done that work for a system similar to yours, you might as well be throwing darts at a board as not do it! There will be no literature for using the GROMACS 4.6 Verlet kernels, because they're new. So there's something of a burden of proof on people adopting it before the GROMACS authors publish their thoughts on using it. Work in progress. That said, there's no doubting that the Verlet kernels are technically superior to the group kernels, in theory and implementation (as discussed on the page you linked). The case for using Verlet kernels right now is stronger if you don't have much water, want good energy conservation, or anticipate a long-term need for strong scaling to lots of hardware. You've no alternative if you want to use GPUs. 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
Re: [gmx-users] Re: gInstallation Problems with Gromacs4.6
Hello Mark
Sorry for the misunderstanding. Actually i did not provide any extra flags
to cmake. I generally edit the CMakeCache.txt file to provide the proper
paths. I somehow felt that was easier to do. I didn't think that could
lead to errors. I have installed gromacs 4.6 on multiple systems using the
same procedure, same mpi and fftw versions, using shared libraries, but
only on HPC i got the mentioned error. So you can imagine my surprise on
getting such an error. And i was more surprised when it got configured
successfully on disabling the shared library flag. If there is problem
with cmake then i expect it, to give the same error irrespective of
whether i enable shared libraries or not. Just my thoughts.
With Regards
Abhishek
By asking how you calling cmake I mean that cmake takes a number of
command-line options, and since using those inappropriately (or not
calling
the right MPI wrapper compiler) might cause symptoms like yours, we need
more complete information to have a chance of helping solve your problem.
Christoph also asked for your cmake command line.
Mark
On Mon, Mar 4, 2013 at 9:04 PM, Abhishek Acharya
aacha...@iitk.ac.inwrote:
OK, but that still might not be fixing the real problem, which might
be
starting with how you are calling cmake in the first place.
Mark
Actually, i called the cmake-2.8.10 which i had installed in my home
directory as the one installed on the cluster was an old version.
so i cd to the cmake-build directory and gave the full path to the cmake
executable.
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake ..
I don't understand how this could have caused any installation problem.
Before this i also tried to use the older version cmake installed on the
cluster but that also gave me the same error.
In any case, gromacs4.6 got installed properly by disabling shared
libraries and is up and running. Though i would be interested in knowing
if its possible to remove this error in any other way.
with regards
Abhishek
On Sat, Mar 2, 2013 at 7:20 AM, Abhishek Acharya
aacha...@iitk.ac.inwrote:
Date: Fri, 1 Mar 2013 23:59:36 +0530
From: Abhishek Acharya aacha...@iitk.ac.in
Subject: [gmx-users] Installation Problems with Gromacs4.6
To: gromacs maillist gmx-users@gromacs.org
Message-ID:
2ca7063e41d6ddfa7ea411dc3cfe3ad3.squir...@webmail.iitk.ac.in
Content-Type: text/plain;charset=iso-8859-1
Hello Gromacs Users.
I have been trying to install Gromacs4.6 on our HPC facility. I
think
I
have correctly provided all the necessary mpi and fftw library
paths.
But
when i try to run configure it gives me the following error:
CMake Error at cmake/FindFFTW.cmake:105 (message):
Could not find fftwf_plan_r2r_1d in
/home/aacharya/softwares/fftw-3.3.3/lib/libfftw3f.so, take a
look
at
the
error message in
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeError.log
to
find out what went wrong. If you are using a static lib (.a)
make
sure
you
have specified all dependencies of fftw3f in FFTWF_LIBRARY by
hand
(e.g.
-DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):
CMakeLists.txt:894 (find_package)
As suggested here I looked into the CMakeError.log file of which I
can't
make any sense.
Source file was:
#include mpi.h
int main(void) {
void* buf;
MPI_Allreduce(MPI_IN_PLACE, buf, 10, MPI_FLOAT, MPI_SUM,
MPI_COMM_WORLD);
}
Determining if the function fftwf_plan_r2r_1d exists in the
/home/aacharya/softwares/fftw-3.3.3/lib failed with the following
output:
Change Dir:
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/gmake cmTryCompileExec2668319475/fast
/usr/bin/gmake -f
CMakeFiles/cmTryCompileExec2668319475.dir/build.make
CMakeFiles/cmTryCompileExec2668319475.dir/build
gmake[1]: Entering directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E
cmake_progress_report
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp/CMakeFiles
1
Building C object
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
/usr/bin/cc -Wextra -Wno-missing-field-initializers
-Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d -o
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
-c
/home/aacharya/softwares/cmake-2.8.10.2/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec2668319475
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E
cmake_link_script
CMakeFiles/cmTryCompileExec2668319475.dir/link.txt --verbose=1
/usr/bin/cc -Wextra -Wno-missing-field-initializers
-Wno-sign-compare
-Wall -Wno-unused -Wunused-value
Re: [gmx-users] g_hbond and contact
I am sorry There is no 7ws Its a typographic error. What I wanted to ask was - I am comparing two simulations S1 and S2 for contacts at a given cut off I used g_mdmat and g_hbond to calculate it. g_hbond outputs: of -num and -hbn was considered. 1. -hbn output was analysed to calculate how many contacts each atom has from both S1 and S2. 2. -num output graph was compared from both S1 and S2. g_mdmat output: of -no was considered. 3. -no output was analysed from both S1 and S2 using the third column or the second Y value which gives total contacts of each atom. It was observed that 1 and 3 matched exactly giving the same number of contacts each atom has (in the whole simulations). indicating that the number of contacts each atom has was more in S2 than S1. But the graph from 2 indicated that the number of contacts (along the trajectory) in S1 was higher than S2. My doubt is: The number of contact per atom follows S2 S1 while number of contacts per time follows S1 S2. I am unclear as to what I have to conclude from this observations. - I used the same cutoff throughout. - There has not been any swapping of the trajectory while analysing. Thank you Kavya On Tue, Mar 5, 2013 at 1:09 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 1:10 PM, Kavyashree M wrote: On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote: When measuring contacts, you don't measure one group, you measure the number of contacts that occur between groups A and B, which considers all atoms in those two groups. I gave a group of hydrophobic atoms in both cases The command I gave - g_hbond_46 -fx.xtc-s x.tpr-contact -n x.ndx -r 0.4 -hbm o.xpm -hbn o.ndx -num o.xvg my index file contained a group of hydrophobic atoms. which I supplied in the x.ndx. You don't define contacts in an index group, you define atoms that may or may not make contacts with others. The one I mentioned here is the output index file from the g_hbond (4.6 version) - o.ndx. [ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_*** *CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5292 5296 530 There's something very wrong with this index file. How did you generate it? The presence of a repeated atom number (5) and a nonsensical one (7ws) leads me to believe that you've done something incorrect. Did this come from g_hbond? It looks like the output of -hbn, which is only useful for decoding hbmap.xpm, nothing else. I did not generate this. The tool (g_hbond) generated this index file. It is the -hbn output. OK, then I still don't know what 7ws is, but the only purpose for this file is to provide a key to the existence matrix in hbmap.xpm. Your previous description indicated that you were using it for some other analysis, which would not be appropriate. The other thing worth mentioning here is something that was posted to the list just a few hours ago, that the output of g_hbond -contact may not agree with other methods of calculating contacts, especially in the case of -merge vs. -nomerge. -Justin From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 Total/mean @ legend string 1 Total @ legend string 2 Mean @ legend string 3 # atoms @ legend string 4 Mean/# atoms #resratio tot mean natm mean/atm 1 1.001 1110.991110.991 2 1.244 10 8.0411 8.041 3 1.166 1311.147111.147 4 1.036 1110.615110.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. That shouldn't be unexpected. Two independent simulations have no guarantee of doing the same thing, that's why sampling is so important. Thank you kavya -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use
