[gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition
First of all, thanks a lot guys, in special Ilja and Chris. Indeed, Ilja's observation proved to be corrected, and as Chris suggested, using the pdb instead of the gro for grompp and the energies matched. However, I am still uneasy with the fact that pdb2gmx_d and mdrun_d is not generating a gro with at least 6 decimals instead of the usual 3. Many thanks, Alan On Tue, Jul 27, 2010 at 20:34, gmx-users-requ...@gromacs.org wrote: Alan: you should try Ilja's suggestion, it was a good one. The idea is that during pdb2gmx you may have obtained a .gro file that was rounded and then you may have used this .gro as input to grompp and so your run did not start with the exact same coordinates in gromacs and namd. A similar test would be to be sure that you run grompp with the same .pdb file that you used in namd, etc. (or perhaps you already did that?) Actually, from what you post below I think that you have your answer. Use the orig .pdb into grompp and things should be ok, probably even in single precision, although the output .gro will be rounded as you see. PS: let's keep a positive mood. Chris. -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Entropy from NMA
Hi, Can you post the exact commands you used for EM and NMA? Ran nahren manuel wrote: Dear Gromacs Users, I am trying to calculate Entropy from Normal Mode Analysis. I minimized the structure to 8.41750710592449e-09 Then I calculated the normal mode (the mdp file is given below). But when i try to calculate the Eigenvalues, I get the following warning One of the lowest 6 eigenvalues has a non-zero value. This could mean that the reference structure was not properly energy minimized. Writing eigenvalues... I get only negative eigenvalues. Let me also add that I used the same mdp file for minimization changing the integrator to steep, cg and finally to l-bfgs. Best, nahren --- integrator= nm constraints = none define = -DFLEXIBLE emtol= 0.0001 emstep = 0.0001 nsteps= 5 nstlist= 1 ns_type= grid rlist= 1.5 coulombtype= shift rcoulomb-switch= 1.0 rvdw-switch= 1.0 vdwtype = shift rcoulomb = 1.3 rvdw = 1.3 -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] [nonbond_params] section , choice of parameters
Hi All, I want to exclude attractive Lennard-Jones interactions between atoms that i defined in the ffamber99nb.itp file. the properties of the dummy atom which I defined are: *amber99_69X 0. 0. A 3.39967e-01 3.59824e-02* ; (i.e., Sigma=3.39967e-01 and Epsilon=3.59824e-02) So , to exclude the attractive LJ term i added [nonbond_params] section as following: *[ nonbond_params ] ; i j func c6 c12 amber99_69 amber99_69 1 0.0E-00 0.34252E-06* (I set c6 to zero to eliminate the attractive LJ term..(or at least that is what i was thinking) ) I have a problem though: apparently from the simulation, *there is no repulsion at all between the atoms*, as i see the atoms overlapping each other.. i guess that something is wrong with the choice of c12, not sure though. the manual says (page 98), if I understand correctly: C(12) = 4*Epsilon*Sigma^12 (hence, *0.34252E-06 = 4* ** 3.59824e-02*(** 3.39967e-01**)^12) *can someone let me know how to fix this problem (i.e., just get rid of the attractive terms according to the parameters above)? is the syntax i used for the nonbond_params OK? Many Thanks, amir -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Entropy from NMA
p.s. How big is this negative value? Ran Friedman wrote: Hi, Can you post the exact commands you used for EM and NMA? Ran nahren manuel wrote: Dear Gromacs Users, I am trying to calculate Entropy from Normal Mode Analysis. I minimized the structure to 8.41750710592449e-09 Then I calculated the normal mode (the mdp file is given below). But when i try to calculate the Eigenvalues, I get the following warning One of the lowest 6 eigenvalues has a non-zero value. This could mean that the reference structure was not properly energy minimized. Writing eigenvalues... I get only negative eigenvalues. Let me also add that I used the same mdp file for minimization changing the integrator to steep, cg and finally to l-bfgs. Best, nahren --- integrator= nm constraints = none define = -DFLEXIBLE emtol= 0.0001 emstep = 0.0001 nsteps= 5 nstlist= 1 ns_type= grid rlist= 1.5 coulombtype= shift rcoulomb-switch= 1.0 rvdw-switch= 1.0 vdwtype = shift rcoulomb = 1.3 rvdw = 1.3 -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition
Hi, The gro file format, just like the pdb format, is an ancient fixed format. Thus it supports only 3 decimals. Note that this has nothing to do with single or double precision (which have a range of rougly 10^7 and 10^16). If pdb2gmx does not mess with your hydrogen and terminal atom coordinates (as some old versions did), you can use pdb2gmx -o conf.pdb for pdb coordinate output or -o conf.g96 for lots of decimals. All Gromacs programs can read pdb and g96 instead of gro files. Berk From: alanwil...@gmail.com Date: Wed, 28 Jul 2010 07:45:50 +0100 To: gmx-users@gromacs.org Subject: [gmx-users] Re: gromacs energies very different from other MD engine for the very same system and condition First of all, thanks a lot guys, in special Ilja and Chris. Indeed, Ilja's observation proved to be corrected, and as Chris suggested, using the pdb instead of the gro for grompp and the energies matched. However, I am still uneasy with the fact that pdb2gmx_d and mdrun_d is not generating a gro with at least 6 decimals instead of the usual 3. Many thanks, Alan On Tue, Jul 27, 2010 at 20:34, gmx-users-requ...@gromacs.org wrote: Alan: you should try Ilja's suggestion, it was a good one. The idea is that during pdb2gmx you may have obtained a .gro file that was rounded and then you may have used this .gro as input to grompp and so your run did not start with the exact same coordinates in gromacs and namd. A similar test would be to be sure that you run grompp with the same .pdb file that you used in namd, etc. (or perhaps you already did that?) Actually, from what you post below I think that you have your answer. Use the orig .pdb into grompp and things should be ok, probably even in single precision, although the output .gro will be rounded as you see. PS: let's keep a positive mood. Chris. -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] mean square displacement frequency
Hi Greg, So you want a distribution of MSD, right? I have trajectories which has been obtained from simulating 20,000 atoms in NVT simulation for 25ns. I recorded the trajectory every 3ps which means that I have 60,000 data points per atom. 25000/3 = 8333 Where do these 60k per atom come from? I am trying to construct a histogram where y-axis is the frequency (# of atoms) and x-axis is the mean square displacement over 25ns. I think a simple way to achieve this by looking at individual atoms and calculate its msd over 25ns and put them in a bin. But there are 20,000 atoms there and 60,000 data points per atom which makes me hard to do this on a spreadsheet -- even if I cut down the data points for each atoms by two orders of magnitude, I have to deal with 12 million data points. g_rmsf gives you sqrt(MSD) per atom. That should bring you quite close to what you need. Also give the manual a read once (more); there's many more tools that can do all kinds of things that may at some point be useful. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Entropy from NMA
Dear Ran, I ran the whole NMA again and I found where I go wrong. I hope it will help others as well. (sorry for a big email) In steps 1 2 (of minimization) I kept the C-alpha frozen. 1. doublegrompp -f em1.mdp -c r1dodecapdb.pdb -p r1top.top -o em1tpr.tpr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em1tpr Steepest Descents converged to Fmax 100 in 2569 steps Potential Energy = -6.21296128286120e+03 Maximum force = 9.87358378592302e+01 on atom 701 Norm of force = 1.04875323563923e+01 2. doublegrompp -f em2.mdp -c em1tpr.gro -p r1top.top -o em2tpr.tpr -t em1tpr.trr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em2tpr Polak-Ribiere Conjugate Gradients converged to Fmax 1 in 6596 steps Potential Energy = -7.56682084795001e+03 Maximum force = 9.92719787231560e-01 on atom 1320 Norm of force = 6.47772253797808e-02 3. doublegrompp -f em3.mdp -c em2tpr.gro -p r1top.top -o em3tpr.tpr -t em2tpr.trr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em3tpr Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 writing lowest energy coordinates. Steepest Descents converged to machine precision in 3018 steps, but did not reach the requested Fmax 10. Potential Energy = -8.49398064549505e+03 Maximum force = 6.86336687926682e+01 on atom 935 Norm of force = 7.15798864024085e+00 4. doublegrompp -f em4.mdp -c em3tpr.gro -p r1top.top -o em4tpr.tpr -t em3tpr.trr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em4tpr Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 0.01 writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to machine precision in 21674 steps, but did not reach the requested Fmax 0.01. Potential Energy = -9.66058047638671e+03 Maximum force = 1.49342602818840e+00 on atom 590 Norm of force = 1.86576579430541e-01 5.doublegrompp -f em5.mdp -c em4tpr.gro -p r1top.top -o em5tpr.tpr -t em4tpr.trr ~/gmxdpr/bin/doublemdrun -v -deffnm em5tpr Low-Memory BFGS Minimizer converged to machine precision in 10346 steps, but did not reach the requested Fmax 0.0001. Potential Energy = -9.66337416273684e+03 Maximum force = 6.48625019025464e-04 on atom 581 Norm of force = 6.35632681200205e-05 6.doublegrompp -f em6.mdp -c em5tpr.gro -p r1top.top -o em6tpr.tpr -t em5tpr.trr Low-Memory BFGS Minimizer converged to machine precision in 3316 steps, but did not reach the requested Fmax 1e-08. Potential Energy = -9.66337416275038e+03 Maximum force = 6.48788529801368e-05 on atom 8 Norm of force = 6.56362137550289e-06 7. doublegrompp -f em7.mdp -c em6tpr.gro -p r1top.top -o em7tpr.tpr -t em6tpr.trr Low-Memory BFGS Minimizer converged to machine precision in 7530 steps, but did not reach the requested Fmax 1e-08. Potential Energy = -9.66337416275071e+03 Maximum force = 4.07762128402886e-07 on atom 10 Norm of force = 5.79534451487287e-08 8. doublegrompp -f em8.mdp -c em7tpr.gro -p r1top.top -o em8tpr.tpr -t em7tpr.trr Low-Memory BFGS Minimizer converged to Fmax 1e-08 in 5840 steps Potential Energy = -9.66337416275070e+03 Maximum force = 8.41750710592449e-09 on atom 521 Norm of force = 1.2888919393e-09 NMA 9. doublegrompp -f nma.mdp -t em8tpr.trr -c em8tpr.gro -p r1top.top -o nmatpr.tpr ~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr (a sinlge processor) ~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr it created only one nmatpr.mtx Maximum force: 8.41751e-09 Finished step 1400 out of 1400 It creates the output nmatpr.mtx nmatpr.edr etc Now I delete all nma files rm nmatpr.* (4 processor) mpirun -np 4 ~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr Maximum force: 8.41768e-09 Maximum force: 8.41768e-09 Maximum force: 8.41768e-09 Maximum force: 8.41768e-09 Finished step 1399 out of 1400 Writing Hessian... Writing Hessian... Writing Hessian... Finished step 1400 out of 1400 Writing Hessian... Back Off! I just backed up nmatpr.mtx to ./#nmatpr.mtx.2# It gives me negative eigenvalues. One would expect it should not create nmatpr.mtx.1 nmatpr.mtc.2 etc...since these files have been removed. Because it created multiple nmatpr.mtx file and backup one over another I am not sure If the problem occurs with my system , but other MPIRUN (with mdrun) do not create such backup. Best, nahren --- On Wed, 7/28/10, Ran Friedman r.fried...@bioc.uzh.ch wrote: From: Ran Friedman r.fried...@bioc.uzh.ch Subject: Re: [gmx-users] Entropy from NMA To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, July 28, 2010, 3:10 PM p.s. How big is this negative value? Ran Friedman wrote: Hi, Can you post the exact commands you used for EM and NMA? Ran nahren manuel wrote: Dear Gromacs Users, I am trying to calculate Entropy from Normal Mode Analysis. I minimized the
[gmx-users] RE: [nonbond_params] section , choice of parameters
Hi Amir,
Are you sure you're giving the parameters indeed as C_6 and C_{12}?
According to the combination rule in the [ defaults ] section, you may
be giving the two parameters directly as sigma and epsilon; sigma=0 (as
well as epsilon=0) would give an identically zero potential . See
sections 5.3.3 and 5.7.1 in the manual (version 4.0).
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Re: [gmx-users] RE: [nonbond_params] section , choice of parameters
Hi Ehud,
Did you mean that i can simply specify Sigma and Epsilon?
The thing is that i didn't want to obtain a zero potential , but rather
maintain the repulsive term of the LJ interaction.
What would you specify then, for the C6 and C12 parameters?
Amir
On Wed, Jul 28, 2010 at 3:00 PM, Ehud Schreiber schr...@compugen.co.ilwrote:
Hi Amir,
Are you sure you’re giving the parameters indeed as C_6 and C_{12}?
According to the combination rule in the [ defaults ] section, you may be
giving the two parameters directly as sigma and epsilon; sigma=0 (as well as
epsilon=0) would give an identically zero potential . See sections 5.3.3 and
5.7.1 in the manual (version 4.0).
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Re: [gmx-users] Re: NPT and NVT simulations
I put the constraints on PA-NE to keep the bond length 3.5 A. After calculating the g_dist I noted that the bond length is atound 5.5 A. Can you tell why its taking 5.5 A. If I difine contraints=all-bonds in mdp file then it shows 3.5 A proper bond length. Can u tell where is the problem. Here I pasted the .itp file ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_997 PA 0 100.1.000 A0.4e-01 0.82890e-01 opls_998 NE 0 100. -1.000 A0.4e-01 0.82890e-01 [ bondtypes ] ; ij func b0 kb PANE 10.35 00 [ moleculetype ] ; name nrexcl ABC 2 [ atoms ] ; nr typeresnr residu atomcgnrcharge mass 1 opls_9971 ABCPA 11. 100. 2 opls_9981 ABCNE 1 -1. 100.000 [ constraints ] ; ij func b0 kb 12 10.35 On Tue, July 27, 2010 7:07 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Can you tell where I am going worng. Here I pasted my .itp file ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5 0.5 ; comb-rule 3 is square-root sigma, the OPLSAA version [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_997 PA 0 100.1.000 A0.4e-01 0.82890e-01 opls_998 NE 0 100. -1.000 A0.4e-01 0.82890e-01 [ constraints ] ; ij func b0 kb 12 10.35 As I said before (and is explained in the manual), [constraints], like any other bonded parameter, must belong to a [moleculetype], which you have not defined here. You've got atom types and force field information, but no molecule to which the constraints are applied. -Justin Nilesh On Tue, July 27, 2010 12:38 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: still I am getting the same error. Now I added this two lines [ constraints ] 1 2 10.35 Then you still have the directive in the wrong place. -Justin On Tue, July 27, 2010 12:34 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: I am using opls force field. I have solvent.itp file. I added follwing line in my solvent.itp file. [ constraints ] opls_997 opls_998 10.35 I am getting the following error You don't define constraints with atom types, you use atom numbers. See the manual. Fatal error: Syntax error - File solvent.itp, line 13 Last line read: ' [ constraints ]' Invalid order for directive constraints Then you've put it in the wrong place. Like any other bonded term, [constraints] belongs to the moleculetype to which the constraint is to be applied. -Justin Nilesh On Tue, July 27, 2010 11:29 am, Justin A. Lemkul wrote: Yes, if you define it in a [ constraints ] directive, and use constraints = none in your .mdp file, so that other bonds will not be converted to constraints, but the one you explicitly set in the topology will be used. -Justin Nilesh Dhumal wrote: Can I put constraint on selected bond? Nilesh On Sun, July 25, 2010 11:33 pm, Vitaly Chaban wrote: 1. Using freezegrps is not generally a good idea to fix a bond length. Look at the constraints mechenism better. Or just try a bigger force constant in topology. 2. NPT and freezegrps do not interact correctly, since freezegrps just freezes any changes of atom positions, so they are not rescaled even if the box size is changed in NPT. 3. Anyway, I think you have defined incorrect groups if your atoms of interest are still movable. Check a diffusion constant of your bonded atoms, it should be zero in the case of freezegrps. Dr. Vitaly Chaban I am trying to freeze a bond (3.5 A) in my system. I used the index file to define group and I added this two lines in my .mdp file. freezegrps = PA NE freezedim = Y Y Y Y Y Y I used g_dist to verify the distance between the freezing atoms. During the NVT simulation the distace is around 3.449 A and its constant though out the simulation. For NPT simulation the distance varies from 3.449 to 3.1. Can you tell why distance changes in NPT not in NVT. How can I freeze a bond om NPT simulation? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] RE: [nonbond_params] section , choice of parameters
Hello,
the method I know to obtain just a repulsive LJ potential is to
calculate the minimum of the potential, then set the cut-off to the
minimum and shift the whole potential by the amount of the minimum. Then
you just have a repulsive LJ interaction. However as soon as more than
one particle type is involved you will run into problems with this
method, because different cutoffs will arise. So it will be necessary to
form tables and use them.
/Flo
On 28.07.10 14:31, Amir Marcovitz wrote:
Hi Ehud,
Did you mean that i can simply specify Sigma and Epsilon?
The thing is that i didn't want to obtain a zero potential , but
rather maintain the repulsive term of the LJ interaction.
What would you specify then, for the C6 and C12 parameters?
Amir
On Wed, Jul 28, 2010 at 3:00 PM, Ehud Schreiber
schr...@compugen.co.il mailto:schr...@compugen.co.il wrote:
Hi Amir,
Are you sure you’re giving the parameters indeed as C_6 and C_{12}?
According to the combination rule in the [ defaults ] section, you
may be giving the two parameters directly as sigma and epsilon;
sigma=0 (as well as epsilon=0) would give an identically zero
potential . See sections 5.3.3 and 5.7.1 in the manual (version 4.0).
--
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Re: [gmx-users] Entropy from NMA
Dear Ran and Nahren, I run into a similar problem a couple of weeks ago: http://lists.gromacs.org/pipermail/gmx-users/2010-July/052377.html In short, integrator = steep can be run in parallel. Output from parallel and single-node are equal. integrator = l-bfgs runs only in single-node, as advertised in the manual. mdrun dies with a fatal error if one tries to run in parallel: Fatal error: Cannot do parallel L-BFGS Minimization - yet. integrator = nm runs in parallel without any error. However, output is wrong: mdrun write multiple hessian.mtx files, each with small size. mdrun seems to get in to some kind of race condition, because sometimes only one .mtx is produced (still, with small size). Running g_nmeig in these parallel mtx results in huge all-negative eigenvalues. The same input in single-node goes just fine, with first 6 eigenvalues close to zero. Rui Rodrigues On Wed, 28 Jul 2010 12:55:44 +0200, Ran Friedman wrote Your NMA seem to run on one processor four times. I'm not sure if the EM part can be run in parallel. This doesn't seem to be the reason for the negative eigenvalue. What was the g_anaeig command (with flags)? nahren manuel wrote: Dear Ran, I ran the whole NMA again and I found where I go wrong. I hope it will help others as well. (sorry for a big email) In steps 1 2 (of minimization) I kept the C-alpha frozen. 1. doublegrompp -f em1.mdp -c r1dodecapdb.pdb -p r1top.top -o em1tpr.tpr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em1tpr Steepest Descents converged to Fmax 100 in 2569 steps Potential Energy = -6.21296128286120e+03 Maximum force = 9.87358378592302e+01 on atom 701 Norm of force = 1.04875323563923e+01 2. doublegrompp -f em2.mdp -c em1tpr.gro -p r1top.top -o em2tpr.tpr -t em1tpr.trr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em2tpr Polak-Ribiere Conjugate Gradients converged to Fmax 1 in 6596 steps Potential Energy = -7.56682084795001e+03 Maximum force = 9.92719787231560e-01 on atom 1320 Norm of force = 6.47772253797808e-02 3. doublegrompp -f em3.mdp -c em2tpr.gro -p r1top.top -o em3tpr.tpr -t em2tpr.trr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em3tpr Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 writing lowest energy coordinates. Steepest Descents converged to machine precision in 3018 steps, but did not reach the requested Fmax 10. Potential Energy = -8.49398064549505e+03 Maximum force = 6.86336687926682e+01 on atom 935 Norm of force = 7.15798864024085e+00 4. doublegrompp -f em4.mdp -c em3tpr.gro -p r1top.top -o em4tpr.tpr -t em3tpr.trr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em4tpr Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 0.01 writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to machine precision in 21674 steps, but did not reach the requested Fmax 0.01. Potential Energy = -9.66058047638671e+03 Maximum force = 1.49342602818840e+00 on atom 590 Norm of force = 1.86576579430541e-01 5.doublegrompp -f em5.mdp -c em4tpr.gro -p r1top.top -o em5tpr.tpr -t em4tpr.trr ~/gmxdpr/bin/doublemdrun -v -deffnm em5tpr Low-Memory BFGS Minimizer converged to machine precision in 10346 steps, but did not reach the requested Fmax 0.0001. Potential Energy = -9.66337416273684e+03 Maximum force = 6.48625019025464e-04 on atom 581 Norm of force = 6.35632681200205e-05 6.doublegrompp -f em6.mdp -c em5tpr.gro -p r1top.top -o em6tpr.tpr -t em5tpr.trr Low-Memory BFGS Minimizer converged to machine precision in 3316 steps, but did not reach the requested Fmax 1e-08. Potential Energy = -9.66337416275038e+03 Maximum force = 6.48788529801368e-05 on atom 8 Norm of force = 6.56362137550289e-06 7. doublegrompp -f em7.mdp -c em6tpr.gro -p r1top.top -o em7tpr.tpr -t em6tpr.trr Low-Memory BFGS Minimizer converged to machine precision in 7530 steps, but did not reach the requested Fmax 1e-08. Potential Energy = -9.66337416275071e+03 Maximum force = 4.07762128402886e-07 on atom 10 Norm of force = 5.79534451487287e-08 8. doublegrompp -f em8.mdp -c em7tpr.gro -p r1top.top -o em8tpr.tpr -t em7tpr.trr Low-Memory BFGS Minimizer converged to Fmax 1e-08 in 5840 steps Potential Energy = -9.66337416275070e+03 Maximum force = 8.41750710592449e-09 on atom 521 Norm of force = 1.2888919393e-09 NMA 9. doublegrompp -f nma.mdp -t em8tpr.trr -c em8tpr.gro -p r1top.top -o nmatpr.tpr ~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr (a sinlge processor) ~/gmxdpr/bin/doublemdrun -v -deffnm nmatpr it created only one nmatpr.mtx Maximum force: 8.41751e-09 Finished step 1400 out of 1400 It creates
Re: [gmx-users] Entropy from NMA
Dear Rui, Thanks for the info - maybe it's better to submit a bugzilla for the NMA in parallel then, do I'm not sure if this can be checked on run-time with mdrun. From Nahren's description I understood that multiples files were generated and assumed that they were backups (as if you run identical MD multiple times with the same input and files). Ran J. Rui Rodrigues wrote: Dear Ran and Nahren, I run into a similar problem a couple of weeks ago: http://lists.gromacs.org/pipermail/gmx-users/2010-July/052377.html In short, integrator = steep can be run in parallel. Output from parallel and single-node are equal. integrator = l-bfgs runs only in single-node, as advertised in the manual. mdrun dies with a fatal error if one tries to run in parallel: Fatal error: Cannot do parallel L-BFGS Minimization - yet. integrator = nm runs in parallel without any error. However, output is wrong: mdrun write multiple hessian.mtx files, each with small size. mdrun seems to get in to some kind of race condition, because sometimes only one .mtx is produced (still, with small size). Running g_nmeig in these parallel mtx results in huge all-negative eigenvalues. The same input in single-node goes just fine, with first 6 eigenvalues close to zero. Rui Rodrigues On Wed, 28 Jul 2010 12:55:44 +0200, Ran Friedman wrote Your NMA seem to run on one processor four times. I'm not sure if the EM part can be run in parallel. This doesn't seem to be the reason for the negative eigenvalue. What was the g_anaeig command (with flags)? nahren manuel wrote: Dear Ran, I ran the whole NMA again and I found where I go wrong. I hope it will help others as well. (sorry for a big email) In steps 1 2 (of minimization) I kept the C-alpha frozen. 1. doublegrompp -f em1.mdp -c r1dodecapdb.pdb -p r1top.top -o em1tpr.tpr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em1tpr Steepest Descents converged to Fmax 100 in 2569 steps Potential Energy = -6.21296128286120e+03 Maximum force = 9.87358378592302e+01 on atom 701 Norm of force = 1.04875323563923e+01 2. doublegrompp -f em2.mdp -c em1tpr.gro -p r1top.top -o em2tpr.tpr -t em1tpr.trr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em2tpr Polak-Ribiere Conjugate Gradients converged to Fmax 1 in 6596 steps Potential Energy = -7.56682084795001e+03 Maximum force = 9.92719787231560e-01 on atom 1320 Norm of force = 6.47772253797808e-02 3. doublegrompp -f em3.mdp -c em2tpr.gro -p r1top.top -o em3tpr.tpr -t em2tpr.trr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em3tpr Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 writing lowest energy coordinates. Steepest Descents converged to machine precision in 3018 steps, but did not reach the requested Fmax 10. Potential Energy = -8.49398064549505e+03 Maximum force = 6.86336687926682e+01 on atom 935 Norm of force = 7.15798864024085e+00 4. doublegrompp -f em4.mdp -c em3tpr.gro -p r1top.top -o em4tpr.tpr -t em3tpr.trr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em4tpr Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 0.01 writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to machine precision in 21674 steps, but did not reach the requested Fmax 0.01. Potential Energy = -9.66058047638671e+03 Maximum force = 1.49342602818840e+00 on atom 590 Norm of force = 1.86576579430541e-01 5.doublegrompp -f em5.mdp -c em4tpr.gro -p r1top.top -o em5tpr.tpr -t em4tpr.trr ~/gmxdpr/bin/doublemdrun -v -deffnm em5tpr Low-Memory BFGS Minimizer converged to machine precision in 10346 steps, but did not reach the requested Fmax 0.0001. Potential Energy = -9.66337416273684e+03 Maximum force = 6.48625019025464e-04 on atom 581 Norm of force = 6.35632681200205e-05 6.doublegrompp -f em6.mdp -c em5tpr.gro -p r1top.top -o em6tpr.tpr -t em5tpr.trr Low-Memory BFGS Minimizer converged to machine precision in 3316 steps, but did not reach the requested Fmax 1e-08. Potential Energy = -9.66337416275038e+03 Maximum force = 6.48788529801368e-05 on atom 8 Norm of force = 6.56362137550289e-06 7. doublegrompp -f em7.mdp -c em6tpr.gro -p r1top.top -o em7tpr.tpr -t em6tpr.trr Low-Memory BFGS Minimizer converged to machine precision in 7530 steps, but did not reach the requested Fmax 1e-08. Potential Energy = -9.66337416275071e+03 Maximum force = 4.07762128402886e-07 on atom 10 Norm of force = 5.79534451487287e-08 8. doublegrompp -f em8.mdp -c em7tpr.gro -p r1top.top -o em8tpr.tpr -t em7tpr.trr Low-Memory BFGS Minimizer converged to Fmax 1e-08 in 5840 steps Potential Energy = -9.66337416275070e+03 Maximum force = 8.41750710592449e-09 on atom 521 Norm of force = 1.2888919393e-09 NMA 9.
[gmx-users] RE: RE: [nonbond_params] section , choice of parameters
Hi again,
Yes, you can simply specify sigma and epsilon, but indeed in your case
you do not want to do so but rather to specify C_6 and C_{12} with the
former being zero to avoid attraction.
Your .top file should include a [ defaults ] section, perhaps through an
#include of a .itp file. Perhaps yours is in ffamber99.itp (I don't have
it installed so I can't tell). In this section there are 5 parameters;
the second is a combination rule which must equal 1 for the two
numbers to represent indeed C_6 and C_{12} (see table 5.3, eq. 5.1-5.4,
and in page 112).
In short, check whether the second parameter in the [ defaults ] section
of ffamber99.itp is 1, if not that's probably the problem. Of course, if
you change this you'll screw up all the other parameters, so it seems
you could either change the force field or create your copy of the files
with all the relevant LJ parameters changed to the combination rule=1
convention.
From: Ehud Schreiber
Sent: Wednesday, July 28, 2010 3:01 PM
To: 'gmx-users@gromacs.org'
Subject: RE: [nonbond_params] section , choice of parameters
Hi Amir,
Are you sure you're giving the parameters indeed as C_6 and C_{12}?
According to the combination rule in the [ defaults ] section, you may
be giving the two parameters directly as sigma and epsilon; sigma=0 (as
well as epsilon=0) would give an identically zero potential . See
sections 5.3.3 and 5.7.1 in the manual (version 4.0).
--
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Re: [gmx-users] periodicity and correct output
I think I met the same problem. When apply periodicity to the system, some atoms will translate to the other side of the box, and this gives wrong polarization values (especially in dynamic simulations). Anyone has idea how to prevent this and get correct polarization in dynamics? Thanks, Shuangxing Dai On Mon, Jul 26, 2010 at 12:26 AM, Vitaly Chaban vvcha...@gmail.com wrote: Hi, Is there an option in any gromacs utility to apply periodicity to the output configuration or trajectory? I want to get all the coordinates just within an elementary box, between 0 and LBOX in spite of any details of the system. For example, editconf -no(pbc) does not do its work since after processing negative coordinates are sometimes present as well as those bigger than LBOX. Vitaly Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE: RE: [nonbond_params] section , choice of parameters
Many Thanks Ehud!
I was certainly not aware of that and I'll check it now..
Amir
On Wed, Jul 28, 2010 at 6:22 PM, Ehud Schreiber schr...@compugen.co.ilwrote:
Hi again,
Yes, you can simply specify sigma and epsilon, but indeed in your case you
do not want to do so but rather to specify C_6 and C_{12} with the former
being zero to avoid attraction.
Your .top file should include a [ defaults ] section, perhaps through an
#include of a .itp file. Perhaps yours is in ffamber99.itp (I don’t have it
installed so I can’t tell). In this section there are 5 parameters; the
second is a “combination rule” which must equal 1 for the two numbers to
represent indeed C_6 and C_{12} (see table 5.3, eq. 5.1-5.4, and in page
112).
In short, check whether the second parameter in the [ defaults ] section of
ffamber99.itp is 1, if not that’s probably the problem. Of course, if you
change this you’ll screw up all the other parameters, so it seems you could
either change the force field or create your copy of the files with all the
relevant LJ parameters changed to the “combination rule”=1 convention.
*From:* Ehud Schreiber
*Sent:* Wednesday, July 28, 2010 3:01 PM
*To:* 'gmx-users@gromacs.org'
*Subject:* RE: [nonbond_params] section , choice of parameters
Hi Amir,
Are you sure you’re giving the parameters indeed as C_6 and C_{12}?
According to the combination rule in the [ defaults ] section, you may be
giving the two parameters directly as sigma and epsilon; sigma=0 (as well as
epsilon=0) would give an identically zero potential . See sections 5.3.3 and
5.7.1 in the manual (version 4.0).
--
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Re: [gmx-users] periodicity and correct output
Hi Shuangxing, For my case, I wrote a script just to do +/- LBOX when xLBOX || x 0. I am not well familiar with polarization algorithm in gromacs but it seems not to be a problem during a run since mdrun applies PBC at every step. Maybe I am false here... Vitaly On Wed, Jul 28, 2010 at 6:35 PM, Shuangxing Dai shuangxing...@gmail.com wrote: I think I met the same problem. When apply periodicity to the system, some atoms will translate to the other side of the box, and this gives wrong polarization values (especially in dynamic simulations). Anyone has idea how to prevent this and get correct polarization in dynamics? Thanks, Shuangxing Dai On Mon, Jul 26, 2010 at 12:26 AM, Vitaly Chaban vvcha...@gmail.com wrote: Hi, Is there an option in any gromacs utility to apply periodicity to the output configuration or trajectory? I want to get all the coordinates just within an elementary box, between 0 and LBOX in spite of any details of the system. For example, editconf -no(pbc) does not do its work since after processing negative coordinates are sometimes present as well as those bigger than LBOX. Vitaly Dr. Vitaly Chaban -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mpi installation problems
I am trying to install gromacs with MPI enabled on a cluster but it seems like fftw is giving me trouble. First, I compile everything without MPI just fine. FFTW is already on the cluster. I export pertinent variables... export CPPFLAGS=-I/opt/fftw/3.2.1/include export LDFLAGS=-L/opt/fftw/3.2.1/lib export CC=/opt/intel/Compiler/11.1/069/bin/intel64/icc export F77=/opt/intel/Compiler/11.1/069/bin/intel64/ifort I have been using gromacs without MPI for over a month without any issues. Now, I need to recompile mdrun with MPI. So I use... export MPICC=/opt/intel/mpi/3.1/bin64/mpicc in addition to all the previous exports. Then, I issue the command... ./configure --prefix=/home/username/gromacs --enable-mpi --program-suffix=_mpi --disable-nice --enable-double which runs fine. Then I issue... make mdrun and I end up with a bunch of undefined references. I am copying some of the output here. Also, I do not know if FFTW is compiled with single/double because of unresponsive admins, but I have tried compiling gromacs with both options and still got errors. Also, from a previous post, I read the idea to install FFTW with shared libraries enabled, which I tried but just ended up with other errors. Thanks in advance for any help. I have been at this for weeks. By the way, this might not be critical, but here is some system info # 2 Nodes Share: * 1x 1702 Altus Server (1U, contains 2 Independent Motherboards) # 1x AMD Dual Opteron 2380(Shanghai) 2.5GHz Quad Core (8 Cores) # 250GB SATA2 Hard Drive *output from make mdrun ** /opt/fftw/3.2.1/lib/libfftw3.a(vrank3-transpose.o):vrank3-transpose.c:(.text+0x649): more undefined references to `_inte l_fast_memcpy' follow /opt/fftw/3.2.1/lib/libfftw3.a(vrank3-transpose.o): In function `apply_toms513': vrank3-transpose.c:(.text+0xe3e): undefined reference to `_intel_fast_memset' vrank3-transpose.c:(.text+0xef4): undefined reference to `_intel_fast_memcpy' vrank3-transpose.c:(.text+0xf0e): undefined reference to `_intel_fast_memcpy' vrank3-transpose.c:(.text+0x106d): undefined reference to `_intel_fast_memcpy' vrank3-transpose.c:(.text+0x108a): undefined reference to `_intel_fast_memcpy' vrank3-transpose.c:(.text+0x110d): undefined reference to `_intel_fast_memcpy' /opt/fftw/3.2.1/lib/libfftw3.a(vrank3-transpose.o):vrank3-transpose.c:(.text+0x1122): more undefined references to `_int el_fast_memcpy' follow /opt/fftw/3.2.1/lib/libfftw3.a(dht-rader.o): In function `apply': dht-rader.c:(.text+0x4a8): undefined reference to `_intel_fast_memset' /opt/fftw/3.2.1/lib/libfftw3.a(dht-rader.o): In function `awake': dht-rader.c:(.text+0xaab): undefined reference to `_intel_fast_memset' /opt/fftw/3.2.1/lib/libfftw3.a(cpy1d.o): In function `fftw_cpy1d': cpy1d.c:(.text+0x268): undefined reference to `_intel_fast_memcpy' /opt/fftw/3.2.1/lib/libfftw3.a(cpy2d.o): In function `dotile_buf': cpy2d.c:(.text+0x6a7): undefined reference to `_intel_fast_memcpy' cpy2d.c:(.text+0x129f): undefined reference to `_intel_fast_memcpy' cpy2d.c:(.text+0x1870): undefined reference to `_intel_fast_memcpy' cpy2d.c:(.text+0x1902): undefined reference to `_intel_fast_memcpy' /opt/fftw/3.2.1/lib/libfftw3.a(cpy2d.o):cpy2d.c:(.text+0x22dd): more undefined references to `_intel_fast_memcpy' follow /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Unpack_external' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_get_errhandler' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_start' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_test' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Comm_spawn' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Request_get_status' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `MPIR_Err_return_comm' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Type_dup' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_get_group' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Comm_spawn_multiple' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Free_mem' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `MPIR_Grequest_set_lang_f77' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_create_keyval' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `b_use_gettimeofday' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Type_get_attr' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Close_port' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Comm_create_errhandler' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Query_thread' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Type_match_size' /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Open_port'
[gmx-users] potential git server downtime
Hi, Due to construction work in the university building, the source code repository server git.gromacs.org may experience some downtime on Jul 29/30 (Thu/Fri). Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs energies very different from other MD engine for the very same system and conditions
Hi, On Jul 27, 2010, at 5:06 PM, Ilja Khavrutskii wrote: I think the bond terms differ simply due to the round off error. The gro file is worse than pdb when it comes to round off in Cartesian coordinates. You can confirm this is the case by taking your gro file and converting it back to pdb using gromacs tools and then use the resulting pdb (with the same round of as the gro file now) file from gromacs in NAMD. You should see the same numbers for bonded terms then. It's even more complex than that :-) To accurately compare coordinates (which affect the energy) you might even need to use PDB as input to both programs (grompp can read those too). The problem is that e.g. 15.50 and 1.550 look like a simple factor 10 difference, but remember that floating-point numbers are stored in base-2, and then the difference is no longer exactly a factor 10 (because that can't be expressed in binary). Depending on the gromacs version, make sure you have absolutely identical coordinates, so that none of the programs have modified e.g. terminal hydrogens or oxygens. Gromacs-4.0.x does some stupid things for a few FF's there, but Gromacs-4.5 should keep them entirely clean. I'm not saying errors are impossible, but Eric Sorin has done _very_ extensive validation of all the original Amber parts against the actual Amber package, not only for equilibrium structures but also severely distorted conformations to catch minor errors in functional forms. In fact, he did find one minor program error related to ordering of improper torsions in TPR during his work, but that turned out to be in Amber ;-) Suffice to say, I trust his work a _lot_. Cheers, Erik -- Erik Lindahl lind...@cbr.su.se Professor, Computational Structural Biology Center for Biomembrane Research Swedish e-Science Research Center Department of Biochemistry Biophysics, Stockholm University Tel: +468164675 Cell: +46703844534 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Maximum table size for tabulated non-bonded potential
Hi all, I have large potential tables that I want to work with in Gromacs 4.0.7 but they get cut at reading apparently (even the atom name get cut). The smaller ones read well. I used to have the same table (with a different sign for the force of course) in Gromacs 3.99 CVS (compiled on 2008-05-20). I remember I had to increase a #define constant (max size I guess) at some point for gromacs not to segfault (grompp stage) but I can't remember which one(s)... Gromacs 4.0.7 does not segfault so it is harder for me to figure out which is the #define constant I need to modify. Could anybody help me please? Julie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] compressing the system
Dear Dr.Chaban, I tried to get the same results as you got for density and total energy starting from the 8 chains is the box. I used the revised mdp file and since PME option takes much time I used shift instead for a moment to verify if I can get the density you obtained. Also I used constraints for bonds. density I get after 1800ps is 850 kg/m3 while what you got is a slightly different (after 1000ps density varies around 880!). Also the total energy you have is bout 2300 whereas I get somethong around 12000!. I dont know why they are so different.. In the second trial I used constraints = none just the shift for electrostatics is not the same as the mdp file you suggested. again results are not the same for total energy (2 Kj/mol). Below is the average values...also simulation crashes at 1550 ps and the last density I am getting is 834! still less than what you got. dont really know why results are not the same. The reason simulation crashes could be due to dt=0.002 while removing constraints? I have two more inquiries: 1- What I see is that the system is getting compressed to a size of around 3 3 3 nm is the first 20ps abruptly and in the remainder of time system reaches equilibrium... This is very different approach than what I was trying doing before. I used berendsen scheme for pressure coupling and box reduced is size slowly but I had difficulty reaching the size I want and most of the simulations crashed. Does this mean berenden is not suitable for compressing system for all systems? 2- You said I dont need NVT at all. But if I want to study the system I get from NPT giving the density I want, can I not do NVT for a fixed system size and calcualte energies or other quantities I am after? Thanks for your attention Moeed Energy Average RMSD Fluct. Drift Tot-Drift --- Bond3885.23141.365139.725 0.0478427 74.3668 Angle 5864.23149.886149.885 -0.00114897 -1.78597 Ryckaert-Bell. 2243.62144.068134.737 -0.113664 -176.679 LJ-141167.530.874230.6402 -0.00845667 -13.1451 Coulomb-14 -553.95431.341330.7865 -0.0130831 -20.3364 LJ (SR)-4898.73405.434386.584 -0.272304 -423.27 Coulomb (SR)1250.2256.236156.1252 0.0078672 12.2288 Potential 8958.11379.038344.366 -0.352947 -548.621 Kinetic En. 10834.2156.085156.066 -0.00535835 -8.32903 Total Energy19792.3414.016381.523 -0.358305 -556.95 Temperature 300.0694.322994.32248 -0.000148407 -0.230684 Pressure (bar) 29.58961263.171263.16 0.0112876 17.5454 Box-X 3.674081.722471.70558 -0.000536305 -0.833634 Box-Y 3.51.614821.59898 -0.000502786 -0.781532 Box-Z 2.451261.667351.64995 -0.000535423 -0.832263 Density (SI)815.50472.849170.7123 0.0390324 60.6721 pV 54.9014 2111.12111.07 -0.0208174 -32.3586 Vir-XX 3606.981466.951466.92 0.0213665 33.2121 Box-Vel-XX -0.0182685 0.234428 0.232397 6.8633e-05 0.106683 Mu-Y 0.102393 0.966426 0.966077 -5.79406e-05 -0.0900631 Heat Capacity Cv: 12.4757 J/mol K (factor = 0.000207551) ;Run control integrator = md ; type of dynamics algorithm. Here md uses a leap-frog algorithm for integrating Newtons's eq of motion dt = 0.002 ; in ps ! nsteps = 90 ; length of simulation= nsteps*dt nstcomm = 1 ; frequency for center of mass motion removal ;Output control nstenergy = 100 ; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps nstxout = 100 ; frequency to write coordinates/velocity/force to output trajectory file. how often snapshots are collected= nstxout*dt nstvout = 0 nstfout = 0 nstlog = 1000 ; frequency to write energies to log file nstxtcout = 0 ; frequency to write coordinates to xtc trajectory ;Neighbor searching nstlist = 10 ; frequency to update neighbor list. Neighborlist will be updated at least every 10 steps. Manual p80 ns_type = grid ; make a grid in the box and only check atoms in neighboring grid cells when constructing a new neighbor list every nstlist steps ;Electrostatics/VdW coulombtype = Shift ;PME rev ; tells gromacs how to model
[gmx-users] Re: compressing the system
Dear Moeed: I tried to get the same results as you got for density and total energy starting from the 8 chains is the box. I used the revised mdp file and since PME option takes much time I used shift instead for a moment to verify if I can get the density you obtained. Also I used constraints for bonds. density I get after 1800ps is 850 kg/m3 while what you got is a slightly different (after 1000ps density varies around 880!). Also the total energy you have is bout 2300 whereas I get somethong around 12000!. I dont know why they are so different.. Different methods for electrostatics give very different absolute energies as a result. C'est la vie... In the second trial I used constraints = none just the shift for electrostatics is not the same as the mdp file you suggested. again results are not the same for total energy (2 Kj/mol). Below is the average values...also simulation crashes at 1550 ps and the last density I am getting is 834! still less than what you got. dont really know why results are not the same. Because the methods are not identical. Please read about electrostatics treatment to understand this issue. The reason simulation crashes could be due to dt=0.002 while removing constraints? It can be due to C-H fast oscillations, for example. Maybe it is a good idea to try SHAKE for these bonds if the time-step is so critical for you. 1- What I see is that the system is getting compressed to a size of around 3 3 3 nm is the first 20ps abruptly and in the remainder of time system reaches equilibrium... This is very different approach than what I was trying doing before. I used berendsen scheme for pressure coupling and box reduced is size slowly but I had difficulty reaching the size I want and most of the simulations crashed. Does this mean berenden is not suitable for compressing system for all systems? I did not ever observe that. Please also note that I used semiisotropic pressure coupling for your system because of its specific [rather anisotropic] structure with long molecules. I suppose this option should provide more realistic density in your particular case. 2- You said I dont need NVT at all. But if I want to study the system I get from NPT giving the density I want, can I not do NVT for a fixed system size and calcualte energies or other quantities I am after? Of course, you can. This is the only way to have a constant density. Good luck. Vitaly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
