Re: [gmx-users] Lateral Diffusion of Lipids

for any help ! ~Thu -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http

Re: [gmx-users] g_wham -sym

to know if it is possible to symmetrize the profile around a non-zero point? forexample z=60? Use -zprof0. -Justin -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University

Re: [gmx-users] g_wham error analysis hangs

-- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de

Re: [gmx-users] Error bars - g_wham

significant. How can I impove my error bars? Why they are so large? Steven -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen

Re: [gmx-users] g_wham missing option

. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen

Re: [gmx-users] virtual site generation for backbone hydrogen

Sorry, I found the error. There was a bond -C N missing in the rtp file. Cheers, Jochen Am 12/17/12 5:28 PM, schrieb Jochen Hub: Hi all, I try to generate a topology using pdb2gmx of a protein that contains a non-native amino acid, that is lysine with some more atoms, which is treated a one

[gmx-users] virtual site generation for backbone hydrogen

into residuetypes.dat, and there are entries in the rtp and hdb. Many thanks in advance for any help, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus

Re: [gmx-users] g_wham with pull_geometry=position

Matysiak Biomolecular Modeling Laboratory Fischell Department of Bioengineering University of Maryland, College Park -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University

[gmx-users] Re: [gmx-developers] shell polarizable water model

= 0.1 couple-moltype = couple-lambda0 = vdw-q couple-lambda1 = vdw-q couple-intramol = no userreal4= 0 -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology

Re: [gmx-users] Re: genbox Not enough memory

size). Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark -- --- Dr. Jochen Hub Computational Molecular Biophysics Group

Re: [gmx-users] Re: genbox Not enough memory

ps: There is a fix for this issue in Gerrit code review: https://gerrit.gromacs.org/#/c/1175/ which introduces a fix genbox -allpair. This avoid the memory-leaky neighbor searching, which is the reason for your problem. Jochen Am 10/11/12 10:56 AM, schrieb Jochen Hub: Hi, this is due

[gmx-users] PhD position in Göttingen/Germany

Dear simulators, we have a PhD position available in the Computational Molecular Biophysics group in Göttingen (Germany). Please have a look here for more details: http://cmb.bio.uni-goettingen.de/jobs.html Thank you, Jochen -- --- Dr. Jochen

Re: [gmx-users] Bootstrapping using g_wham

/Mailing_Lists -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http

Re: [gmx-users] Force constant in g_wham

recall reading somewhere that the force constant sometimes includes the (1/2) term in front of K_i, and sometimes not. Thank you, Lili -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg

[gmx-users] rare huge forces in constraint simulation with direction_periodic

in advance, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni

Re: [gmx-users] rare huge forces in constraint simulation with direction_periodic

Sorry, I forgot: I used gmx version 4.5.5-dev. Jochen Am 6/25/12 3:53 PM, schrieb Jochen Hub: Hi, I am running a constraint simulation, with 12 molecules restrained with respect to the center of mass of a lipid membrane. During 5ns of simulation, I get a few frames (e.g. 10 or so) with huge

Re: [gmx-users] Umbrella sampling PMF, drug and membrane with pull_geometry=cylinder

work just fine. So this will be the way for now at least. Guess that there could be an error in the inout parsing then. Thanks a lot for your help, really appreciate it. -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute

[gmx-users] Structures and topologies of cholesterol-containing membranes

amounts of cholesterol are available. Please feel free to use them if they are relevant for your research (we only ask to cite our papers). Happy simulating, Jochen -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute

Re: [gmx-users] g_wham position 0

experienced this problem before? I'm hoping it's just some minor issue in g_wham. I even invoked the -zprof0 flag to - zprof 0 and it did not set my PMF curve to start at 0. Sincerely, Lili -- --- Dr. Jochen Hub Computational Molecular Biophysics Group

Re: [gmx-users] Statistical error of Umbrella Sampling

-- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de

Re: [gmx-users] g_wham with cylinder geometry

Users Forum mailing list archive at Nabble.com. -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49

Re: [gmx-users] Umbrella sampling and WHAM along a curved pathway?

like to calculate the PMF along a curved reaction pathway using umbrella sampling. I just wonder if it is appropriate to use g_wham to extract the PMF along the curved pathway? Any help would be appreciated. Hao Jiang -- --- Dr. Jochen Hub

Re: [gmx-users] Spherical constraint (spherical force)

-- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html

Re: [gmx-users] GPUs and umbrella sampling

-- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html

Re: [gmx-users] error bars g_wham

in bsResult.xvg (option -bsres), not in profile.xvg. Cheers, Jochen -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http

Re: [gmx-users] g_traj -ox -com slight inconsistency

of operations or precision. The same results exist for at least 4.0.5 and 4.5.3. Thanks, Chris. -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18

Re: [gmx-users] g_wham PMF profile

- A free weighted histogram analysis implementation including robust error and autocorrelation estimates J. Chem. Theory Comput. 6 pp. 3713-3720 (2010) Cheers, Jochen -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular

Re: [gmx-users] Zero Potential of Mean Force with g_wham

get a non-zero PMF curve. I assume that there is something going on with g_wham on version 4.5.1. Thank you for your help. Susana On Wed, Mar 9, 2011 at 3:00 PM, Mark Abraham Mark.Abraham at anu.edu.auwrote: -- --- Dr. Jochen Hub Computational

Re: [gmx-users] WHAM with multiple force constants

). -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- gmx-users mailing list

[gmx-users] harmonic restraint with OpenMM

-- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html

Re: [gmx-users] g_wham: Pull geometry direction_periodic not supported

On 9/18/10 Sep 18,10:17 PM, Jochen Hub wrote: On 9/10/10 Sep 10,2:40 PM, Eudes Fileti wrote: Hi gmx-users I finished a series of pulling runs using the periodic_direction option and when I run the g_wham analysis I received the following message

Re: [gmx-users] OPLS-AA force field

-NH+, How can I deal with this? Any suggestion is appreciated. Thanks in advance. -- wende -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46

Re: [gmx-users] Split pmf

attention! -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html

Re: [gmx-users] g_wham: Pull geometry direction_periodic not supported

Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 http://fileti.ufabc.edu.br -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala

Re: [gmx-users] Can I make make_ndx interactive?

a C_O OC q EOF -f nn_1.pdb try: cat EOF | make_ndx -f prot.pdb a C_O q EOF Jochen but -flags doesn't seem to be recognized. Does anyone know a work around? Thanks Jenny -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

them with -ip to g_wham. That will certainly require a bit of scripting, but should not be too difficult. Make sure to get the direction (plus/minus z) right when turning the distance in the pullx into pdo files with z as reaction coordinate. Good luck, Jochen Tom Jochen Hub wrote: Thomas

Re: [gmx-users] PMF of ligand transport

. Jochen I am getting a plot , but potential is increasing constantly. ie, PMF is not converged as mentioned the tutorial? Do I need to extend the sampling ? or any other reason? Please help me. Thank you. -Aswathy -- --- Dr. Jochen Hub

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

as using the pullf.xvg files as input to g_wham. I apologise if I am missing something obvious (or doing something silly!) but any help would be greatly appreciated. Cheers Tom -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

and -max the -noauto option would have been the 'correct' way to do this. Cheers Tom Jochen Hub wrote: Thomas Piggot wrote: Hi, I am trying to construct a PMF profile for a phosphate ion passing through a membrane protein using umbrella sampling with GROMACS 4.0.5. I have performed the umbrella

Re: [gmx-users] g_wham gets stuck

constants. Just make sure that the order of tpr and pullx files agree in the -it and -ix input agree. Jochen amir On Fri, Apr 30, 2010 at 4:00 PM, Jochen Hub joc...@xray.bmc.uu.se mailto:joc...@xray.bmc.uu.se wrote: Justin A. Lemkul wrote: Amir Marcovitz wrote

Re: [gmx-users] g_wham gets stuck

se. The only criterion is that you have generated configurations from which you can derive reasonably-spaced windows in which you do sufficient sampling. -Justin Again, Thanks a lot for the quick reply Amir On Thu, Apr 29, 2010 at 10:33 AM, Jochen Hub joc...@xray.bmc.uu.se mailto:joc

Re: [gmx-users] g_wham gets stuck

the problem? this is really frustrating.. need your help, Amir -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755

Re: [gmx-users] g_wham giving flat free energy

know what could cause this? Hi Micheal, how large is your data? Could you send me a tar.gz of your pdo files? I would like to make sure that there is no bug in g_wham. Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell

Re: [gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

to the present directory and largely increase the respective vdw radii in that file (e.g. the carbon radii) before running genbox. Best, Jochen Thanks for helping! Rasoul -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell

Re: [gmx-users] Concerns with g_wham

=umbrella but pull=constraint. You should get the same PMF compared to umbrella sampling and using g_wham. Please let me know if g_wham makes any trouble. Cheers, Jochen Thank you, Jennifer -- --- Dr. Jochen Hub Molecular Biophysics group Dept

Re: [gmx-users] slow speed

typically do neighbor searching every 10 to 20 fs. Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755

Re: [gmx-users] mean force.

-- wende -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- gmx

Re: [gmx-users] make ghost atom

Laboratory P.O. Box 2008, MS-6372 Oak Ridge, TN 37831 Phone (865) 241-1482 E-mail pa...@ornl.gov -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18

Re: [gmx-users] g_wham error

Thanks for the help Gard -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755

Re: [gmx-users] PMF of large protein

: +46 (0)90-7865368 -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755

Re: [gmx-users] Problems wtih g_wham

g_wham to get the PMF. Best wishes, Jochen I have attached my original pull .mdp file, and the .mdp file used in the 14 equilibration runs. I appreciate any help. Thanks, Jenny -- --- Dr. Jochen Hub Molecular Biophysics group Dept

[gmx-users] valgrind warnigs with git mdrun

== To see them, rerun with: --leak-check=full --show-reachable=yes ==6218== ==6218== For counts of detected and suppressed errors, rerun with: -v ==6218== ERROR SUMMARY: 252186 errors from 21 contexts (suppressed: 4 from 4) -- --- Dr. Jochen Hub Molecular

[gmx-users] linking gromcs to efence

. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] New tutorial available - umbrella sampling

this instructional material will help out. -Justin -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755

Re: [gmx-users] Error while pulling a settled tip4p water molecule

rechecked with xxdiff, the two settle lines are the same. Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755

[gmx-users] Error while pulling a settled tip4p water molecule

I do not really understand the suggestions, change the least use settle constraints into 3 normal constraints, why do I have to replace the settle constraint? Cheers, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell

Re: [gmx-users] Error while pulling a settled tip4p water molecule

constraint? Cheers, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755

Re: [gmx-users] Error while pulling a settled tip4p water molecule

Then there is something odd. The two settles are definitely identical since I simply copied the tip4p.itp. I also just rechecked with xxdiff, the two settle lines are the same. Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell

Re: [gmx-users] water molecule not settled.........

out...? the same system when i run in previous version of gromacs it showed wrote pdb files with previous current coordinates segmentation fault, what is the reason behind this difference in error ? -- --- Dr. Jochen Hub

Re: [gmx-users] Simulation at unrealistic temperatures

-- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Disulfide bridge formation between A and B state

-- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- gmx-users mailing list

Re: [gmx-users] Disulfide bridge formation between A and B state

, that's why I am surprised that there seems to be no solution for that. Or am I missing something here? Any ideas? Thanks a lot, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala

[gmx-users] FEP with bond formation, pair problem

-- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- -- gmx-users mailing list

Re: [gmx-users] FEP with bond formation, pair problem

the coulomb 1-4 interaction can be explicitly given. Thanks a lot for any help, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden

Re: [gmx-users] vsites and lincs-order

(4-5 fs, with vsites). Has anyone experience how severe that issue is. Has anyone observed artefacts with lincs-order=4 and large time steps? Thanks a lot, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group

Re: [gmx-users] LINCS error

interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden

[gmx-users] vsites and lincs-order

. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ gmx-users mailing listgmx-users

Re: [gmx-users] vsites and lincs-order

is. Has anyone observed artefacts with lincs-order=4 and large time steps? Thanks a lot, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone

Re: [gmx-users] large VCM(group rest)

. 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 -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124

Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes

crashed, but much later (after 11ns), that why I just noticed that. I have repeated the simulations now to make really sure that the crashes are reproducible. Jochen Jochen Hub wrote: I have only tested on 8 nodes, and 4 x 2 x 1 DD. Should I try

Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes

the simulations now to make really sure that the crashes are reproducible. Jochen Jochen Hub wrote: I have only tested on 8 nodes, and 4 x 2 x 1 DD. Should I try someting else? Jochen Berk Hess wrote: Hi, One question: Are these crashes

[gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes

-- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ gmx-users mailing

Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes

-- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ gmx

Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes

to every atom? 2) Is a bug report appreciated on that issue? Best, Jochen -- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18

Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes

Hey Berk, I just found that the simulation with a separate CG on each atom also crashed, but much later (after 11ns), that why I just noticed that. I have repeated the simulations now to make really sure that the crashes are reproducible. Jochen Jochen Hub wrote: I have only tested on 8

Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes

are reproducible. Jochen Jochen Hub wrote: I have only tested on 8 nodes, and 4 x 2 x 1 DD. Should I try someting else? Jochen Berk Hess wrote: Hi, One question: Are these crashes single processor, with domain decomposition, or both? Berk Date: Wed, 30 Sep 2009 15:35:42

Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes

with a separate CG on each atom also crashed, but much later (after 11ns), that why I just noticed that. I have repeated the simulations now to make really sure that the crashes are reproducible. Jochen Jochen Hub wrote: I have only tested on 8 nodes, and 4 x 2 x 1 DD. Should I try

[gmx-users] read_eigenvectors not in libgmxana

to eigio.o and eigenvectors.o, which is, however, less convenient... Is there a special reason why the routines from eigio.c and eigenvectors.c are not in any library? Or do I miss something here? Best, Jochen -- --- Dr. Jochen Hub Molecular

Re: [gmx-users] g_wham error

-- --- Dr. Jochen Hub Molecular Biophysics group Dept. of Cell Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4714451 Fax: +46-18-511755 --- ___ gmx-users mailing list

Re: [gmx-users] ffgmx:diffusion of oxygen

. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users

Re: [gmx-users] intermolecular distance restraint

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 -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular

Re: [gmx-users] how to define the dummy atoms in gromacs

. -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312

Re: [gmx-users] how to save grace out put to jpeg or grafifal pic

to eps, and then using the imagemagick command convert -density 100 plot.eps plot.png jochen -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany

Re: [gmx-users] about g_wham

-- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312

Re: [gmx-users] Rugged dgdl curve in turning off/on the charge for Leu

-- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312

Re: [gmx-users] error in parallel mdrun

-- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312

Re: [gmx-users] Bugs in gromacs 4

://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Dr. Jochen Hub Max Planck

Re: [gmx-users] problems with editconf 4.0

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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck

Re: [gmx-users] Misunderstandings with g_rms

. -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312

Re: [gmx-users] Repeating the simulation

. -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx

Re: [gmx-users] problem in prest.mdp file

don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational

Re: [gmx-users] Warning with L-BFGS minimization

On 10/24/08, Jochen Hub [EMAIL PROTECTED] wrote: Hi, with l-bfgs minimzation, grompp always reports WARNING 1 [file em.mdp, line unknown]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. even if the mdp gives ; Method for doing electrostatics coulombtype

Re: [gmx-users] Is it the correct label on Y axis ( density graph)

Mark Abraham wrote: Jochen Hub wrote: huan wrote: Dear all, I am wondering that is it the correct label of y axis in the density graph which i obtained using g_energy? because it is not a density unit but is labeled as kJ/mol Dear huan, 1) I would encourage you to read a few

Re: [gmx-users] density graph ( density vs time)

it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany

Re: [gmx-users] density graph ( density vs time)

. -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312

Re: [gmx-users]Simulated annealing

posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry

[gmx-users] Warning with L-BFGS minimization

= 1. I could't find anything on that in the archive. Is that a known issue? Cheers, Jochen -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen

Re: [gmx-users] Warning with L-BFGS minimization

Mark Abraham wrote: Jochen Hub wrote: Hi, with l-bfgs minimzation, grompp always reports WARNING 1 [file em.mdp, line unknown]: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. even if the mdp gives ; Method for doing electrostatics coulombtype

Re: [gmx-users] spliting clusters.pdb

/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312

Re: [gmx-users] trjconv in Parallel run

. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D

  1   2   >