Re: [gmx-users] energy minimization output
26 sep 2012 kl. 08.16 skrev Shima Arasteh: > Dear all, > > My system contains lipids, protein and water. > I want to energy minimize it, so ran grompp: > > > # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr > > and then: > # mdrun -v -deffnm em > > > The output is: > Steepest Descents: >Tolerance (Fmax) = 1.0e+03 >Number of steps=5 > Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 > Stepsize too small, or no change in energy. > Converged to machine precision, > but not to the requested precision Fmax < 1000 > > Double precision normally gives you higher accuracy. > You might need to increase your constraint accuracy, or turn > off constraints alltogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Back Off! I just backed up em.gro to ./#em.gro.3# > > Steepest Descents converged to machine precision in 15 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = 2.3000388e+17 > Maximum force =inf on atom 518 > Norm of force =inf > > > Why the maximum force and norm of it is not written? I repeated it for a few > times, but no difference. > > It's written. Unfortunately it's infinite. > > Thanks for your suggestions in advance. > Sincerely, > Shima > -- > 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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] energy minimization output
Dear Erik, I also encountered similar problem. So you mean it cannot be further energy minimized? How can we proceed with NPT if the system is not in equilibrium? On Wed, Sep 26, 2012 at 1:11 PM, Erik Marklund wrote: > > 26 sep 2012 kl. 08.16 skrev Shima Arasteh: > > > Dear all, > > > > My system contains lipids, protein and water. > > I want to energy minimize it, so ran grompp: > > > > > > # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr > > > > and then: > > # mdrun -v -deffnm em > > > > > > The output is: > > Steepest Descents: > >Tolerance (Fmax) = 1.0e+03 > >Number of steps=5 > > Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, > atom= 518 > > Stepsize too small, or no change in energy. > > Converged to machine precision, > > but not to the requested precision Fmax < 1000 > > > > Double precision normally gives you higher accuracy. > > You might need to increase your constraint accuracy, or turn > > off constraints alltogether (set constraints = none in mdp file) > > > > writing lowest energy coordinates. > > > > Back Off! I just backed up em.gro to ./#em.gro.3# > > > > Steepest Descents converged to machine precision in 15 steps, > > but did not reach the requested Fmax < 1000. > > Potential Energy = 2.3000388e+17 > > Maximum force =inf on atom 518 > > Norm of force =inf > > > > > > Why the maximum force and norm of it is not written? I repeated it for a > few times, but no difference. > > > > > > It's written. Unfortunately it's infinite. > > > > > Thanks for your suggestions in advance. > > Sincerely, > > Shima > > -- > > 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 > > --- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:+46 18 471 6688fax: +46 18 511 755 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > -- > 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 > -- Archana Sonawani-Jagtap Junior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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] energy minimization output
It seems that your input structure has too severe clashes for energy minimization, that there are problems with your topology, or that your mdp options are not adequate. One possible solution, if your topology is correct, is to first perform an energy minimization using soft-core potentials to get rid of some of the structural strain. In any case you should inspect your structure closely, in particular near atom 518. Erik 26 sep 2012 kl. 10.23 skrev Archana Sonawani: > Dear Erik, > > I also encountered similar problem. So you mean it cannot be further energy > minimized? How can we proceed with NPT if the system is not in equilibrium? > > On Wed, Sep 26, 2012 at 1:11 PM, Erik Marklund wrote: > >> >> 26 sep 2012 kl. 08.16 skrev Shima Arasteh: >> >>> Dear all, >>> >>> My system contains lipids, protein and water. >>> I want to energy minimize it, so ran grompp: >>> >>> >>> # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr >>> >>> and then: >>> # mdrun -v -deffnm em >>> >>> >>> The output is: >>> Steepest Descents: >>> Tolerance (Fmax) = 1.0e+03 >>> Number of steps=5 >>> Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, >> atom= 518 >>> Stepsize too small, or no change in energy. >>> Converged to machine precision, >>> but not to the requested precision Fmax < 1000 >>> >>> Double precision normally gives you higher accuracy. >>> You might need to increase your constraint accuracy, or turn >>> off constraints alltogether (set constraints = none in mdp file) >>> >>> writing lowest energy coordinates. >>> >>> Back Off! I just backed up em.gro to ./#em.gro.3# >>> >>> Steepest Descents converged to machine precision in 15 steps, >>> but did not reach the requested Fmax < 1000. >>> Potential Energy = 2.3000388e+17 >>> Maximum force =inf on atom 518 >>> Norm of force =inf >>> >>> >>> Why the maximum force and norm of it is not written? I repeated it for a >> few times, but no difference. >>> >>> >> >> It's written. Unfortunately it's infinite. >> >>> >>> Thanks for your suggestions in advance. >>> Sincerely, >>> Shima >>> -- >>> 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 >> >> --- >> Erik Marklund, PhD >> Dept. of Cell and Molecular Biology, Uppsala University. >> Husargatan 3, Box 596,75124 Uppsala, Sweden >> phone:+46 18 471 6688fax: +46 18 511 755 >> er...@xray.bmc.uu.se >> http://www2.icm.uu.se/molbio/elflab/index.html >> >> -- >> 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 >> > > > > -- > Archana Sonawani-Jagtap > Junior Research Fellow, > Biomedical Informatics Centre, > NIRRH (ICMR), Parel > Mumbai, India. > 9960791339 > -- > 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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_tcaf segmentation fault
Dear all, I am attempting to calculate the viscosity of a liquid binary system of 500 molecules (3050 atoms), via g_tcaf command. The system is equilibrated. The list of command I use is: /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log// //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg/ The result is a Segmentation fault error: /Selected 0: 'System'// //trn version: GMX_trn_file (single precision)// //Last frame -1 time0.000/*/ /**/Segmentation fault/* I use GROMACS 4.5.5 What am I doing wrong? Thanks in advance Stelios -- -- Stelios Karozis Research Assistant Environmental Research Lab IN-RAS-TES - NCSR Demokritos - Greece email: skaro...@ipta.demokritos.gr tel : 0030 210 650 3403 -- 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] Impropers in OPLS-AA
Hi all, I'm trying to build a topology file for a new molecule (benzimidazole) with the OPLS-AA force field, and I'm confused about which dihedrals and impropers I should include. I'm assuming that the molecule is similar enough to indole and adenine/guanine to use their parameters (except maybe their atomic charges, but I'll disregard this for the moment). I've decided to build an .rtp file and use pdb2gmx to create the topology. All is fine with bonds, angles and dihedrals, I think. In the .rtp I include the atomtypes and bonds, and all connected angles and dihedrals are automatically generated, and I guess that's the right thing here. But which impropers should I include? (I mean, what is the default in OPLS-AA, or what is it "designed" for). I've tried to find it in the OPLS literature, but couldn't find a clear indication of which exact terms to include in a (arbitrary) molecule. I tried to look at the TRP residue in the aminoacids.rtp file, but it only raised some doubts: 1. There are no defined impropers around the bridge atoms CD2 and CE2. 2. Each improper has the central atom as the 3rd atom, and not the 2nd, as the macro names suggest (improper_Z_CA_X_Y). Maybe this does not matter? So, can anyone tell me (or point me to somewhere where I can read it) whether I should include *all* impropers around aromatic atoms and which is the right order for OPLS-AA? Thanks, Ignacio -- 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] something wrong with BlueGene/P
Hi, all, I did many simulations with Gromacs on CO2 Water mixtures on my workstation with 8 cores in parallel, the results are pretty good. For bigger simulations, I turned to the BlueGene machine. The problem is that with exactly the same configuration files and same number of MPI tasks( 8 here) , I always got the following problems. 1773 1774 step 6870: Water molecule starting at atom 1375 can not be settled. 1775 Check for bad contacts and/or reduce the timestep if appropriate. 1776 Wrote pdb files with previous and current coordinates 1777 1778 Step 6871, time 6.871 (ps) LINCS WARNING 1779 relative constraint deviation after LINCS: 1780 rms 0.139809, max 0.559153 (between atoms 10 and 11) 1781 bonds that rotated more than 30 degrees: 1782 atom 1 atom 2 angle previous, current, constraint length 1783 10 11 78.50.1210 0.1813 0.1163 1784 10 12 90.00.1523 0.1152 0.1163 1785 1786 step 6871: Water molecule starting at atom 4576 can not be settled. 1787 Check for bad contacts and/or reduce the timestep if appropriate. 1788 1789 step 6871: Water molecule starting at atom 5794 can not be settled. 1790 Check for bad contacts and/or reduce the timestep if appropriate. 1791 Wrote pdb files with previous and current coordinates 1792 Wrote pdb files with previous and current coordinates 1793 1794 --- 1795 Program mdrun_bgp_d, VERSION 4.5.5 1796 Source code file: pme.c, line: 538 1797 1798 Fatal error: 1799 3 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. 1800 This usually means that your system is not well equilibrated. 1801 For more information and tips for troubleshooting, please check the GROMACS 1802 website at http://www.gromacs.org/Documentation/Errors When I do the energy minimization or the NVT equilibration, Gromacs worked pretty well. The problem happened when I turned to the NPT equilibration. The pressure and temperature were set to be 100bar and 318K respectively. When during the NPT equlibration, the temperature and pressure keep increasing before the program halt. 1161 1162 DD step 6499 load imb.: force 6.9% 1163 1164Step Time Lambda 116565006.50.0 1166 1167Energies (kJ/mol) 1168 AngleLJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 1169 4.50025e+012.21540e+04 -7.02187e+02 -1.23033e+05 -1.27743e+04 1170 PotentialKinetic En. Total EnergyTemperature Pres. DC (bar) 1171-1.14310e+051.50736e+04 -9.92368e+043.74677e+02 -3.36430e+02 1172 Pressure (bar) Constr. rmsd 1173 1.53825e+031.53151e-06 1174 1175 DD step 6599 load imb.: force 5.1% 1176 1177Step Time Lambda 117866006.60.0 1179 1180Energies (kJ/mol) 1181 AngleLJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 1182 5.41207e+012.32123e+04 -7.01221e+02 -1.23852e+05 -1.27349e+04 1183 PotentialKinetic En. Total EnergyTemperature Pres. DC (bar) 1184-1.14022e+051.50532e+04 -9.89688e+043.82147e+02 -3.35505e+02 1185 Pressure (bar) Constr. rmsd 1186 2.37940e+031.40409e-06 1187 1188 DD step 6699 load imb.: force 4.8% 1189 1190Step Time Lambda 119167006.70.0 1192 1193Energies (kJ/mol) 1194 AngleLJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 1195 4.70219e+012.37867e+04 -6.99910e+02 -1.24021e+05 -1.26862e+04 1196 PotentialKinetic En. Total EnergyTemperature Pres. DC (bar) 1197-1.13574e+051.54884e+04 -9.80852e+044.03537e+02 -3.34252e+02 1198 Pressure (bar) Constr. rmsd 1199 3.01172e+031.56366e-06 1200 1201 DD step 6799 load imb.: force 6.7% 1202 1203Step Time Lambda 120468006.80.0 1205 1206Energies (kJ/mol) 1207 AngleLJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 1208 3.79031e+012.70730e+04 -6.97586e+02 -1.24088e+05 -1.24549e+04 1209 PotentialKinetic En. Total EnergyTemperature Pres. DC (bar) 1210-1.10129e+053.49837e+04 -7.51454e+041.00845e+03 -3.32036e+02 1211 Pressure (bar) Constr. rmsd 1212 9.09741e+033.89773e-06 The input file for the NPT equilibration is as follows. define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator ; integrator = md-vv ; leap-frog integrator nsteps = 10 ; 2 * 5 = 100
[gmx-users] Experiences with Gromacs scaling on US supercomputer centers?
Hi all, I'd be interested to know about people's experiences with Gromacs on US national computing centers. Which machines have it set up to scale the best? We're putting in an XSEDE request soon, and I'm trying to figure out which resource to request. Our system is semi-coarse-grained, using reaction field electrostatics, so we don't have to worry about PME. Of course, couldn't hurt to know about PME scaling as well. I'm interesting scalings with 100K - 300K atoms. Of course, best performance will probably change with 4.6 because of all the setup tweaks, but let's start with 4.5 scaling info! Best, Michael Shirts Assistant Professor Department of Chemical Engineering University of Virginia michael.shi...@virginia.edu (434)-243-1821 -- 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_tcaf segmentation fault
On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: > Dear all, > > I am attempting to calculate the viscosity of a liquid binary system of > 500 molecules (3050 atoms), via g_tcaf command. > The system is equilibrated. The list of command I use is: > > /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v > eigenvec.trr -av average.pdb -l covar.log// > //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n > index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of > tcaf_fit.xvg/ -dt 0.001 ? > > The result is a Segmentation fault error: > > /Selected 0: 'System'// > //trn version: GMX_trn_file (single precision)// > //Last frame -1 time0.000/*/ > /**/Segmentation fault/* > > I use GROMACS 4.5.5 > > What am I doing wrong? > > Thanks in advance > Stelios > -- 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] Experiences with Gromacs scaling on US supercomputer centers?
On 2012-09-26 16:24, Michael Shirts wrote: Hi all, I'd be interested to know about people's experiences with Gromacs on US national computing centers. Which machines have it set up to scale the best? We're putting in an XSEDE request soon, and I'm trying to figure out which resource to request. Our system is semi-coarse-grained, using reaction field electrostatics, so we don't have to worry about PME. Of course, couldn't hurt to know about PME scaling as well. I'm interesting scalings with 100K - 300K atoms. Of course, best performance will probably change with 4.6 because of all the setup tweaks, but let's start with 4.5 scaling info! I guess you're aware of Roland Schulz' paper on cellulose systems on Jaguar? Over 100 million particles on 100,000 cores. We have done virus particles (1.2 million particles) on 2000 Cray XE6 cores (in Sweden). You are probably aware that scaling is different for different systems, in particular if you don't have waters. Your systems are relatively small for the big US computers of course, but it is often allowed to do ensemble calculations. I would suggest you get a test account for scaling tests for your particular system. Best, Michael Shirts Assistant Professor Department of Chemical Engineering University of Virginia michael.shi...@virginia.edu (434)-243-1821 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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: Fast exchanges for REMD
Dear all,
I could finally demux my REMD trajectories with high EAF. They look
fine, but I'm not 100% sure about it.
Unfortunately, there seems to be a "bug" in mdrun. As you migh know, the
log files contain the exchange attempts like:
Replica exchange at step 2000 time 4
Repl ex 0123 x 45
Repl pr.00 1.0
However, the time value (4 in this example) is limited to 6 digits. It's
not really a bug because I think GROMACS recommends EAFs of max. 1/ps.
But if you exchange every 0.5 ps (EAF= 2/ps) you can run the simulation
for max. 9 ps only. Otherwise your log will simply chop the time
after the decimal point, e.g.
Replica exchange at step ... time 9.5
...
Replica exchange at step ... time 10
...
Replica exchange at step ... time 10
...
Replica exchange at step ... time 11
...
I have written a Perl script which fixes the time values, based on the given
number of steps and stepsize. Additionally the demux.pl script was changed
because it also chops after 6 digits. I simply changed:
printf(NDX "%-20g",$t);
in the "pr_order" and "pr_revorder" subroutines to:
printf(NDX "%-20.2f",$t);
and it works just fine.
Like I said the trajectories look fine, but I'm not really sure if it's
actually correct that way. I would be happy if anyone would like to discuss
this :)
Cheers,
Andi
Am 24.09.2012 08:49, schrieb Andreas Zink:
Dear all,
I've done some REMD simulations using a quite high exchange attempt
frequency (10 attempts per ps) as proposed by Sindhikara et al.
("Exchange Often and Properly in Replica Exchange Molecular
Dynamics",J. Chem. Theory Comput. 2010, 6, 2804–2808 ).
Unfortunately, I have now recognized that the demux perl script cannot
account for an EAF which is higher than the saving frequency in the
trajectory.
Comments from demux.pl:
# If your exchange was every N ps and you saved every M ps you can
make for
# the missing frames by setting extra to (N/M - 1). If N/M is not
integer,
# you're out of luck and you will not be able to demux your
trajectories at all.
In my case exchanges every 0.1 ps and saved every 5 ps
Changing the demux.pl script, so that it writes the
"replica_index.xvg" with a higher precision (time in ps) should be no
problem. However, my question is: will this work together with trjcat?
Does trjcat search for the timeframe given in the first column of
"replica_index.xvg", or does it links each line to one saved
timeframe? If so, could I just delete the additional lines in
"replica_index.xvg"?
I would be really happy if someone could help me with this!
Thanks!
Andi
--
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: Fast exchanges for REMD
> However, the time value (4 in this example) is limited to 6 digits.
Sounds like this should be increased? There's a pending change to
replica exchange, so this could be added to 4.6 without disrupting the
release timing.
On Wed, Sep 26, 2012 at 11:22 AM, Andreas Zink wrote:
> Dear all,
>
> I could finally demux my REMD trajectories with high EAF. They look fine,
> but I'm not 100% sure about it.
>
> Unfortunately, there seems to be a "bug" in mdrun. As you migh know, the log
> files contain the exchange attempts like:
>>
>> Replica exchange at step 2000 time 4
>> Repl ex 0123 x 45
>> Repl pr.00 1.0
>
> However, the time value (4 in this example) is limited to 6 digits. It's not
> really a bug because I think GROMACS recommends EAFs of max. 1/ps. But if
> you exchange every 0.5 ps (EAF= 2/ps) you can run the simulation for max.
> 9 ps only. Otherwise your log will simply chop the time after the
> decimal point, e.g.
>
>> Replica exchange at step ... time 9.5
>> ...
>>
>> Replica exchange at step ... time 10
>> ...
>>
>> Replica exchange at step ... time 10
>> ...
>>
>> Replica exchange at step ... time 11
>> ...
>
> I have written a Perl script which fixes the time values, based on the given
> number of steps and stepsize. Additionally the demux.pl script was changed
> because it also chops after 6 digits. I simply changed:
>>
>> printf(NDX "%-20g",$t);
>
> in the "pr_order" and "pr_revorder" subroutines to:
>>
>> printf(NDX "%-20.2f",$t);
>
> and it works just fine.
>
> Like I said the trajectories look fine, but I'm not really sure if it's
> actually correct that way. I would be happy if anyone would like to discuss
> this :)
>
>
> Cheers,
>
> Andi
>
>
>
>
> Am 24.09.2012 08:49, schrieb Andreas Zink:
>
>> Dear all,
>>
>> I've done some REMD simulations using a quite high exchange attempt
>> frequency (10 attempts per ps) as proposed by Sindhikara et al. ("Exchange
>> Often and Properly in Replica Exchange Molecular Dynamics",J. Chem. Theory
>> Comput. 2010, 6, 2804–2808 ).
>> Unfortunately, I have now recognized that the demux perl script cannot
>> account for an EAF which is higher than the saving frequency in the
>> trajectory.
>>
>> Comments from demux.pl:
>> # If your exchange was every N ps and you saved every M ps you can make
>> for
>> # the missing frames by setting extra to (N/M - 1). If N/M is not integer,
>> # you're out of luck and you will not be able to demux your trajectories
>> at all.
>>
>> In my case exchanges every 0.1 ps and saved every 5 ps
>>
>> Changing the demux.pl script, so that it writes the "replica_index.xvg"
>> with a higher precision (time in ps) should be no problem. However, my
>> question is: will this work together with trjcat? Does trjcat search for the
>> timeframe given in the first column of "replica_index.xvg", or does it links
>> each line to one saved timeframe? If so, could I just delete the additional
>> lines in "replica_index.xvg"?
>>
>> I would be really happy if someone could help me with this!
>> Thanks!
>>
>> Andi
>>
>
> --
> 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] g_tcaf segmentation fault
The -dt flag is the time step between the frames in ps. I tried the command in any combination i could think of. With -dt without, with -b without, and so on. The only way i get a partial result is to use the .trr file from the simulation and not from the g_covar command and even then i get the density of the system and after that "segmentation fault" Ο χρήστης lina έγραψε: On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: > Dear all, > > I am attempting to calculate the viscosity of a liquid binary system of > 500 molecules (3050 atoms), via g_tcaf command. > The system is equilibrated. The list of command I use is: > > /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v > eigenvec.trr -av average.pdb -l covar.log// > //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n > index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of > tcaf_fit.xvg/ -dt 0.001 ? > > The result is a Segmentation fault error: > > /Selected 0: 'System'// > //trn version: GMX_trn_file (single precision)// > //Last frame -1 time0.000/*/ > /**/Segmentation fault/* > > I use GROMACS 4.5.5 > > What am I doing wrong? > > Thanks in advance > Stelios > -- 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] g_tcaf segmentation fault
On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote: > The -dt flag is the time step between the frames in ps. I tried the command > in any combination i could think of. With -dt without, with -b without, and > so on. The only way i get a partial result is to use the .trr file from the > simulation and not from the g_covar command and even then i get the density > of the system and after that "segmentation fault" > Segmentation fault involves lots. If I were you, I would try -dt 100 or large to reduce memory requirement. or perhaps try the very short time period. namely -e 200 to see what's going on. > Ο χρήστης lina έγραψε: > > On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: >> Dear all, >> >> I am attempting to calculate the viscosity of a liquid binary system of >> 500 molecules (3050 atoms), via g_tcaf command. >> The system is equilibrated. The list of command I use is: >> >> /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v >> eigenvec.trr -av average.pdb -l covar.log// >> //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n >> index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of >> tcaf_fit.xvg/ > > -dt 0.001 ? > >> >> The result is a Segmentation fault error: >> >> /Selected 0: 'System'// >> //trn version: GMX_trn_file (single precision)// >> //Last frame -1 time0.000/*/ >> /**/Segmentation fault/* >> >> I use GROMACS 4.5.5 >> >> What am I doing wrong? >> >> Thanks in advance >> Stelios >> > -- 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_tcaf segmentation fault
Thanks for the suggestion. I just tried and the problem presists. Just to be clear, the right way is to use the g_covar.trr file, correct? Ο χρήστης lina έγραψε: On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote: > The -dt flag is the time step between the frames in ps. I tried the command > in any combination i could think of. With -dt without, with -b without, and > so on. The only way i get a partial result is to use the .trr file from the > simulation and not from the g_covar command and even then i get the density > of the system and after that "segmentation fault" > Segmentation fault involves lots. If I were you, I would try -dt 100 or large to reduce memory requirement. or perhaps try the very short time period. namely -e 200 to see what's going on. > Ο χρήστης lina έγραψε: > > On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: >> Dear all, >> >> I am attempting to calculate the viscosity of a liquid binary system of >> 500 molecules (3050 atoms), via g_tcaf command. >> The system is equilibrated. The list of command I use is: >> >> /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v >> eigenvec.trr -av average.pdb -l covar.log// >> //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n >> index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of >> tcaf_fit.xvg/ > > -dt 0.001 ? > >> >> The result is a Segmentation fault error: >> >> /Selected 0: 'System'// >> //trn version: GMX_trn_file (single precision)// >> //Last frame -1 time0.000/*/ >> /**/Segmentation fault/* >> >> I use GROMACS 4.5.5 >> >> What am I doing wrong? >> >> Thanks in advance >> Stelios >> > -- 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] g_tcaf segmentation fault
On Thursday 27,September,2012 12:55 AM, Stelios Karozis wrote: > Thanks for the suggestion. > I just tried and the problem presists. > Just to be clear, the right way is to use the g_covar.trr file, correct? -f traj.trr InputFull precision trajectory: trr trj cpt Here the full precision means double precision? I see you use single precision. I have never tried this one, perhaps someone else may give you some suggestions. Best regards, > > Ο χρήστης lina έγραψε: > > On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote: >> The -dt flag is the time step between the frames in ps. I tried the command >> in any combination i could think of. With -dt without, with -b without, and >> so on. The only way i get a partial result is to use the .trr file from the >> simulation and not from the g_covar command and even then i get the density >> of the system and after that "segmentation fault" >> > > Segmentation fault involves lots. > If I were you, I would try -dt 100 or large to reduce memory > requirement. or perhaps try the very short time period. namely -e 200 to > see what's going on. > >> Ο χρήστης lina έγραψε: >> >> On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: >>> Dear all, >>> >>> I am attempting to calculate the viscosity of a liquid binary system of >>> 500 molecules (3050 atoms), via g_tcaf command. >>> The system is equilibrated. The list of command I use is: >>> >>> /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v >>> eigenvec.trr -av average.pdb -l covar.log// >>> //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n >>> index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of >>> tcaf_fit.xvg/ >> >> -dt 0.001 ? >> >>> >>> The result is a Segmentation fault error: >>> >>> /Selected 0: 'System'// >>> //trn version: GMX_trn_file (single precision)// >>> //Last frame -1 time0.000/*/ >>> /**/Segmentation fault/* >>> >>> I use GROMACS 4.5.5 >>> >>> What am I doing wrong? >>> >>> Thanks in advance >>> Stelios >>> >> > -- 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_tcaf segmentation fault
On 9/26/12 12:55 PM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the problem presists. Just to be clear, the right way is to use the g_covar.trr file, correct? The trajectory written from g_covar contains eigenvectors from PCA. I don't understand why you would use that here. Use the trajectory from the actual simulation. -Justin Ο χρήστης lina έγραψε: On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote: The -dt flag is the time step between the frames in ps. I tried the command in any combination i could think of. With -dt without, with -b without, and so on. The only way i get a partial result is to use the .trr file from the simulation and not from the g_covar command and even then i get the density of the system and after that "segmentation fault" Segmentation fault involves lots. If I were you, I would try -dt 100 or large to reduce memory requirement. or perhaps try the very short time period. namely -e 200 to see what's going on. Ο χρήστης lina έγραψε: On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: Dear all, I am attempting to calculate the viscosity of a liquid binary system of 500 molecules (3050 atoms), via g_tcaf command. The system is equilibrated. The list of command I use is: /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log// //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg/ -dt 0.001 ? The result is a Segmentation fault error: /Selected 0: 'System'// //trn version: GMX_trn_file (single precision)// //Last frame -1 time0.000/*/ /**/Segmentation fault/* I use GROMACS 4.5.5 What am I doing wrong? Thanks in advance Stelios -- 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] g_tcaf segmentation fault
On 9/26/12 1:12 PM, lina wrote: On Thursday 27,September,2012 12:55 AM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the problem presists. Just to be clear, the right way is to use the g_covar.trr file, correct? -f traj.trr InputFull precision trajectory: trr trj cpt Here the full precision means double precision? I see you use single precision. I have never tried this one, perhaps someone else may give you some suggestions. Full precision and double precision are different, though not completely unrelated in a sense. You can have a single- or double-precision .trr file that is still full precision, all it means is that a different number of decimal points are saved. A .trr has greater precision than an .xtc (independent of a single- or double-precision calculation) simply because it stores more decimal places. -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] g_tcaf segmentation fault
Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation combined with g_anaeig command. So the use of g_covar .trr file as an input, was easy alternative .trr file to see if i will get pass the segmantation fault error. I didn t give it too much thought. Stelios Ο χρήστης Justin Lemkul έγραψε: On 9/26/12 12:55 PM, Stelios Karozis wrote: > Thanks for the suggestion. > I just tried and the problem presists. > Just to be clear, the right way is to use the g_covar.trr file, correct? > The trajectory written from g_covar contains eigenvectors from PCA. I don't understand why you would use that here. Use the trajectory from the actual simulation. -Justin > Ο χρήστης lina έγραψε: > > On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote: >> The -dt flag is the time step between the frames in ps. I tried the command >> in any combination i could think of. With -dt without, with -b without, and >> so on. The only way i get a partial result is to use the .trr file from the >> simulation and not from the g_covar command and even then i get the density >> of the system and after that "segmentation fault" >> > > Segmentation fault involves lots. > If I were you, I would try -dt 100 or large to reduce memory > requirement. or perhaps try the very short time period. namely -e 200 to > see what's going on. > >> Ο χρήστης lina έγραψε: >> >> On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: >>> Dear all, >>> >>> I am attempting to calculate the viscosity of a liquid binary system of >>> 500 molecules (3050 atoms), via g_tcaf command. >>> The system is equilibrated. The list of command I use is: >>> >>> /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v >>> eigenvec.trr -av average.pdb -l covar.log// >>> //g_tcaf -b 0 -e 2 -dt 0.001 -f eigenvec.trr -s topol.tpr -n >>> index.ndx -mol -oc tcaf_cub.xvg -oa tcaf_all.xvg -o tcaf.xvg -of >>> tcaf_fit.xvg/ >> >> -dt 0.001 ? >> >>> >>> The result is a Segmentation fault error: >>> >>> /Selected 0: 'System'// >>> //trn version: GMX_trn_file (single precision)// >>> //Last frame -1 time0.000/*/ >>> /**/Segmentation fault/* >>> >>> I use GROMACS 4.5.5 >>> >>> What am I doing wrong? >>> >>> Thanks in advance >>> Stelios >>> >> > -- 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] g_tcaf segmentation fault
Hi Stelios, Does your .trr file contain velocities? Cheers, Tsjerk On Sep 26, 2012 8:24 PM, "Stelios Karozis" wrote: Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation combined with g_anaeig command. So the use of g_covar .trr file as an input, was easy alternative .trr file to see if i will get pass the segmantation fault error. I didn t give it too much thought. Stelios Ο χρήστης Justin Lemkul έγραψε: On 9/26/12 12:55 PM, Stelios Karozis wrote: > Thanks for the suggestion. > I just tried and the p... The trajectory written from g_covar contains eigenvectors from PCA. I don't understand why you wou... -- Justin A. Lemkul, Ph.D. Research Scientist Department ... -- 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] Intercalation DNA-Ethidium bromide
Dear Gromacs users, I've been running several simulations involving 26 base pairs B-DNA and ethidium bromide. I used Autodock vina for finding inital binding sites and found one in the small groove. After that I ran a simulation of 14 ns. When I check the rmsd of Ethidium Bromide,there's a sudden change. Is there any chance I could see intercalation? P.S. Or I should create an artifical gap between dna bases and then set up a simulation? Thanks in advance, Best regards, Hovakim Grabski-- 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] pca-based MD
Dear all! I've read some reference papers about EDA sampling methods and found such usefull things. First of all as I understood for biassing MD simulation along several PCs extracted from another run the make_edi -radacc 1-3 option is exactly what I need. But I havent still understood about missmatching of atom numbers between EDA (done on C-alpha atoms) and biassed_MD ( all atoms of system including solvent). E.g whan I ve run mdrun I've obtain error Fatal error: Nr of atoms in pca_biased.edi (3075) does not match nr of md atoms (46185) where 3075 is n atoms of my protein (althought I've extracted eigenvectors from c-alpha only) and 46185- full system includding membrane and SOL in that case. Does it mean that such method is only applicable for biassed simulations of the systems in vacuu or with implicit solvent ? James 2012/9/24 James Starlight : > I've still made such 'only c-alpha ensemble' of my structures by the > other software and performed x-ray PCA. As the result I've extracted > eigenvectors and obtained reasonable distribution (projection) of the > structures along that eigenvectors. > > Now I have questions about pca-biassed MD_run. I've made *.edi file > from eigenvectors calculated based on the c-alpha atoms of my x-ray > ensemble. How I could use it with my system consisted of much more > atoms (full atomic protein + solvent) than smaller c-alpha subset of > the x-ray data (only c-alpha atoms from the same protein) ? > i.e if I run mdrun -v -deffnm MD -ei sam.edi > > I obtain error about mismatching of atom number from the edi as well > as system.tpr . > Is there any way to extrapolate number of atoms in the sam.edi ? > > James > > 2012/9/23, James Starlight : >> I've tried to make PCA from my X-ray data and forced with many problems :) >> >> Firstly I've made pdb trajectory in NMR-like format ( by means of >> pymol) consisted of all X-ray structures. >> >> than I've make .tpr file (From the tpr of the same protein which I've >> simulated previously) for the subset of C-alpha atoms common to all >> structures >> >> Finally I've tried to calculate eigenvectors >> Structure or trajectory file has more atoms (2196) than the topology (302) >> >> Does it mean that all structures in trajectory must have only C-alpha >> atoms initialy ? >> >> IS there another way to make tpr as well as pdb trajectory files for >> such x-ray PCA? >> >> >> James >> >> 2012/9/24 Thomas Evangelidis : >>> Hi, >>> >>> thanks again for explanation. Its also intresting to me is it possible to do further biassed MD guided on that FMA modes as well as obtain projections onto that FMA sub-spaces of X-ray datasets for instance ? ( e.g for comparison of the results from FMA of experimental data as well as MD_data) >>> Have a look at another thread posted today, named "PC comparison between >>> two simulations". >>> >>> On a second thought, you might want to consider the nudged elastic band >>> method and its variants for your case, since you have the initial, the >>> final and intermediate states of your protein. Unfortunately they are not >>> implemented in GROMACS, but they are in AMBER. >>> >>> Thomas >>> >>> -- >>> >>> == >>> >>> Thomas Evangelidis >>> >>> PhD student >>> University of Athens >>> Faculty of Pharmacy >>> Department of Pharmaceutical Chemistry >>> Panepistimioupoli-Zografou >>> 157 71 Athens >>> GREECE >>> >>> email: tev...@pharm.uoa.gr >>> >>> teva...@gmail.com >>> >>> >>> website: https://sites.google.com/site/thomasevangelidishomepage/ >>> -- >>> 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
