[gmx-users] where can I download POPC membrane file?

Dear all: I would like to use charmm36 and POPC for membrane protein simulation. and I am wondering where can I download charmm36 pre-pribriumed POPC PDB and topol file for gromacs? Thank you very much Best -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/l

Re:Re: [gmx-users] where can I download POPC membrane file?

ing VMD (VIsual Molecular Dynamics) 2011/5/30 albert Dear all: I would like to use charmm36 and POPC for membrane protein simulation. and I am wondering where can I download charmm36 pre-pribriumed POPC PDB and topol file for gromacs? Thank you very much Best -- gmx-users mailing listgmx-us

[gmx-users] is it possible to convert NAMD psf file to gromacas format?

Hello: I am wondering, is it possible to convert NAMD topol psf file into Gromacs topol format? Thank you very much -- 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/S

Re:Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?

gromacs for non gromacs data. |WARNING ; WARNING| it cannot be used for a simulation. |WARNING At 2011-05-30，"Francesco Oteri" wrote: >Il 29/05/2011 21:58, albert ha scritto: >> Hello: >> I am wondering, is it possible to convert NAMD topol psf file in

Re:Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?

t know if problems would arise for simulation. > > >Il 29/05/2011 22:10, albert ha scritto: >> Thank you very much for kind advices. Here is some warning, and I >> don't know whether there would be some problem or not: >> >> ; 'fake' gromacs topology ge

Re:Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?

difficult to modify them one by one. Thank you very much At 2011-05-30，"Francesco Oteri" wrote: >You can solve the problem without converting from namd to gromacs. >You can use the pdb you've already found to obtain a valid gromacs >topology through pdb2gmx > >

Re:Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?

em. > > >Alternatively,you can replace atom name using some text file editor. > > > > >Il 29/05/2011 22:35, albert ha scritto: >> Well, I also try to do this. But it seem that the atom name in my POPC >> pdb file (which I download from here >> http://terpconnec

Re:Re: Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?

Thank you so much for your kind helps. did you pre-equilibrium it? At 2011-05-30，"Jianguo Li" wrote: Hi Albert, Here is one gro file of 128 POPC lipids which I constructed before using CHARMM36 FF. please check if it is correct before using it. Jianguo From: albert To: Discu

Re:Re: Re: Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?

Thank you so much for your such kind helps. I will try it. At 2011-05-30，"Jianguo Li" wrote: I equilibrated the system for about 20ns at 300K. Jianguo From: albert To: Jianguo Li Cc: Discussion list for GROMACS users Sent: Monday, 30 May 2011 14:52:23 Subject: Re:Re: Re: [gmx-us

Re:Re: Re: Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?

Thank you so much for kind helps. I will try it At 2011-05-30，"Jianguo Li" wrote: I equilibrated the system for about 20ns at 300K. Jianguo From: albert To: Jianguo Li Cc: Discussion list for GROMACS users Sent: Monday, 30 May 2011 14:52:23 Subject: Re:Re: Re: [gmx-users] is i

Re:AW: Re: [gmx-users] where can I download POPC membrane file?

)! http://terpconnect.umd.edu/~jbklauda/research/download.html Von:gmx-users-boun...@gromacs.org im Auftrag von albert Gesendet: So 29.05.2011 21:23 An: Discussion list for GROMACS users Betreff: Re:Re: [gmx-users] where can I download POPC membrane file? But I don't think it is pre-equilibrium POPC mem

Re:Re: AW: Re: [gmx-users] where can I download POPC membrane file?

gt;there is this difference in names. The POPC structure from the link >below still has the atom names of the old CHARMM27 lipids (DPPC is >fine). As suggested, a simple script can do the conversion for you. > >Cheers > >Tom > >albert wrote: >> I know this, but this file

[gmx-users] strange problem with performance information

Hi: I am using the following command to submit gromacs md jobs in cluster: mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum -dlb yes -v -s nvt.tpr" -mode VN -np 128 Then I use command tail -f gromacs.out to check the performance of my jobs and I get the following information:

[gmx-users] another question about performance

Hello: here is my log file for mdrun: Writing final coordinates. step 10, remaining runtime: 0 s Average load imbalance: 10.8 % Part of the total run time spent waiting due to load imbalance: 4.3 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 19 % Z

[gmx-users] nodes error

Hello: I found that each time I would like to increase my nodes for MD run, my job always failed. it said: Will use 192 particle-particle and 64 PME only nodes This is a guess, check the performance at the end of the log file --- Program md

[gmx-users] NPT error

Hi: I am following the tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html the nvt step goes well, but the NPT always doesn't work. it said: Program mdrun_mpi_bg, VERSION 4.5.5 Source code file: ../../../src/mdlib/domdec.c, line: 2633 Fat

[gmx-users] Re: nodes error

thank you very much for kind reply. I change my command as following: mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum -dlb yes -v -s npt.tpr -nt 1" -mode VN -np 256 the "-nt 1" option has been added above. but it still doesn't work and here is the log file Initializing Dom

[gmx-users] Re: Re: nodes error

is there any solution to fix this? THX On 01/06/2012 09:52 AM, gmx-users-requ...@gromacs.org wrote: "The minimum cell size is controlled by the size of the largest charge group or bonded interaction and the largest of rvdw, rlist and rcoulomb, some other effects of bond constraints, and a saf

[gmx-users] NPT error

Hi: I am following the tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html the NVT step goes well, but the NPT always doesn't work. it said: Program mdrun_mpi_bg, VERSION 4.5.5 Source code file: ../../../src/mdlib/domdec.c, line: 2633 Fa

[gmx-users] Nodes problem?

Hello: I am submiting gromacs in cluster and the job ALWAYS terminate with following messages: vol 0.75 imb F 5% pme/F 0.52 step 4200, will finish Sat Jan 7 09:36:14 2012 vol 0.77 imb F 6% pme/F 0.52 step 4300, will finish Sat Jan 7 09:36:28 2012 step 4389: Water molecule starting

[gmx-users] a question about membrane simulation

ect that around 50 ns time scale level, agonist bound GPCR should also expect such kind of side chain switches and it may lost at 100 ns time scale? I would be very appreciated if someone could give me some comments on this issue. Thank you very much best wishes Albert -- gmx-users mailing li

[gmx-users] a question about membrane simulation

ect that around 50 ns time scale level, agonist bound GPCR should also expect such kind of side chain switches and it may lost at 100 ns time scale? I would be very appreciated if someone could give me some comments on this issue. Thank you very much best wishes Albert -- gmx-users mailing li

[gmx-users] dssp error

hello: I am trying to run do_dssp by command: do_dssp -s md.tpr -f md.trr -b 400 -e 500 -o fws_ss.xpm but it said: Select a group: 1 Selected 1: 'Protein' There are 35 residues in your selected group trn version: GMX_trn_file (single precision) Reading frame 400 time 400.000 Back Off! I j

[gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!!

Dear: I am using gromacs for membrane simulation (under CHARMM36 FF) which contains around 80,000 atoms. I've submitted over 200 CPU in the cluster for such system with 2 fs time step. And what really astonished is that the efficiency for such simulation is only 3ns/day. I am wondering what

[gmx-users] how to optimize hydrogen bonds before simulation?

Hello: I am wondering is it possible to optimize hydrogen bonds network before simulation? I've got some crystal solvent in the system and I would like to optimize the hbond network even before building a solvent system. THX -- gmx-users mailing listgmx-users@gromacs.org http://lists.

[gmx-users] Re: do_dssp error

Hello: there is some problem for my do_dssp, it always claimed: Program do_dssp_d, VERSION 4.5.5 Source code file: do_dssp.c, line: 572 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddg1g7Id ddRwthIi > /dev/null 2> /dev/null someone suggest to compile gromacs with double p

[gmx-users] Re: gmx-users Digest, Vol 95, Issue 208

et="us-ascii" And I replied "What's your dssp version? The most recent ones have different flags that are not yet supported by gromacs." Erik 30 mar 2012 kl. 13.23 skrev Albert: Hello: there is some problem for my do_dssp, it always claimed: Program do_dssp_d, VER

[gmx-users] Re: gmx-users Digest, Vol 95, Issue 208

I've tried: 2, 2.1.3, 2.1.4, the problem is still there. I don't think the do_dssp is so difficult. just one command: do_dssp -s md.tpr -f md.trr -b 100 -e 200 -f ss.xpm On 03/30/2012 03:05 PM, Erik Marklund wrote: And what versions were those? 30 mar 2012 kl. 15.06 skrev Alb

[gmx-users] large scale simulation?

Hello: I am wondering does anybody have experience with GROMACS for large scale simulation? I've heard lot of people said that it would be difficult for Gromacs to do so. eg: I've got a 60,000 atoms system, is it possible for GROMACS to produce 100 ns/days or even more? suppose I can use as

[gmx-users] Re: large scale simulation?

ce in Gromacs? Probably each of us can learn a lot from you. thank you very much best Albert -- 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! P

[gmx-users] g_tune_pme error in blue gene

Hello: I am trying to run g_tune_pme in blue gene with following script: # @ job_name = bm # @ class = kdm-large # @ account_no = G07-13 # @ error = gromacs.info # @ output = gromacs.out # @ environment = COPY_ALL # @ wall_clock_limit = 160:00:00 # @ notification = error # @ job_type = bluegen

[gmx-users] another g_tune_pme problem

Hello: I am trying to test g_tune_pme in workstation by command: g_tune_pme_d -v -s md.tpr -o bm.trr -cpi md.cpt -cpo bm.cpt -g bm.log -launch -nt 16 & but it stopped immediately with following logs. I complied gromacs with a -d in each module such as mdrun_d and I aliased mdrun_d to mdrun

[gmx-users] g_cluster for concoord output?

Dear: I've generated a disoc.pdb file by concoord and does any one have any idea how to analyze it by Gromacs g_cluster? when I read the manual of g_cluter, it will require -f traj.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input, Opt. Structur

[gmx-users] jobs failed

Hello: I am using the following script to run Gromacs in cluster, but it failed: # @ job_name = bm # @ class = kdm-large # @ error = gromacs.info # @ output = gromacs.out # @ environment = COPY_ALL # @ wall_clock_limit = 10:00:00 # @ notification = error # @ job_type = bluegene # @ bg_size = 64

[gmx-users] Re: job failed

Hello: thank you very much for kind reply. I tried NVT before I produced NPT MD production. thank you very much -- 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_List

Re: [gmx-users] Re: job failed

hello: thank you very much for your kind messages. I first did minimization, the NVP with gradually heating the system from 0-310K, and them NPT production: NVT.mpd--- define = -DPOSRES -DPOSRES_LIG constraints= hbonds integrator= md dt= 0.001 ; ps !

[gmx-users] where can we obtain the latest Amber ff12SB FF?

hello: I am wondering where can we obtain the latest Amber ff12SB FF for Gromacs? thx -- 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! Pleas

[gmx-users] why it is so slow in Blue gene?

hello: I am running a 60,000 atom system with 128 core in a blue gene cluster. and it is only 1ns/day here is the script I used for submitting jobs: # @ job_name = gmx_test # @ class = kdm-large # @ error = gmx_test.err # @ output = gmx_test.out # @ wall_clock_limit = 00:20:00 # @ job_t

[gmx-users] Re: why it is so slow in Blue gene

es bg_size. Probably I should compile it by myself. Does anybody have any idea how to compile gromacs in blue gene? thank you very much Albert On 04/25/2012 12:31 AM, Dr. Vitaly V. Chaban wrote: hello: I am running a 60,000 atom system with 128 core in a blue gene cluster. and it is on

Re: [gmx-users] why it is so slow in Blue gene?

ffler wrote: On Tue, 24 Apr 2012 15:42:15 +0200 Albert wrote: hello: I am running a 60,000 atom system with 128 core in a blue gene cluster. and it is only 1ns/day here is the script I used for You don't give any information what exact system that is (L/P/Q?), if you run singl

[gmx-users] a question about energygrps

Hello: I am running a membrane simulation with gromacs and I wondering how to deal with energygrps? Should I put protein and lipids into one energygrps? Or I should leave the lipids stay with solvent and ions? thank you very much best Albert -- gmx-users mailing listgmx-users

Re: [gmx-users] a question about energygrps

groups for above paramters in NVT.mdp? thank you very much On 04/25/2012 04:13 PM, Justin A. Lemkul wrote: On 4/25/12 10:07 AM, Albert wrote: Hello: I am running a membrane simulation with gromacs and I wondering how to deal with energygrps? Should I put protein and lipids into one

Re: [gmx-users] a question about energygrps

some one claimed that they can use optimized PMF/F paramters to achieve even 100ns/day for 20,000 atoms system. I also try to use g_tune_pme to get a better performance, but the results are not so satisfied.. Can you give me some advices for this? thank you very much. best Albert On 04

[gmx-users] how to run g_tune_pme in cluster?

Hello: Does anybody have any idea how to run g_tune_pme in a cluster? I tried many times with following command: g_tune_pme_d -v -s npt_01.tpr -o npt_01.trr -cpo npt_01.cpt -g npt_01.log -launch -nt 24 > log & but it always failed. Option Type Value Description

Re: [gmx-users] how to run g_tune_pme in cluster?

rrect mdrun / mpirun executables? Carsten On Apr 26, 2012, at 9:28 AM, Albert wrote: Hello: Does anybody have any idea how to run g_tune_pme in a cluster? I tried many times with following command: g_tune_pme_d -v -s npt_01.tpr -o npt_01.trr -cpo npt_01.cpt -g npt_01.log -launch -nt 24&g

Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

it seesm to be good. just one pieces of advices, why not use CHARMM36 for this tutorial ? since it is the best FF for lipids currently. On 04/26/2012 11:14 AM, Anirban Ghosh wrote: Hi ALL, I have prepared a step-wise tutorial for running a MD simulation of a GPCR protein inserted in a lipid

Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

dification by ourselves. best Albert On 04/26/2012 11:53 AM, Anirban Ghosh wrote: Hello Albert, Thanks. Yes, CHARMM36 indeed handles lipids very well. But currently GROMACS 4.5.5 provides only the option for CHARMM27 FF and I found that ff43a1 very well preserves the characters of both the

Re: [gmx-users] how to run g_tune_pme in cluster?

4.6-dev-20120423-25c75 GIT SHA1 hash:25c752a51955337dc61d80a180ed9efa26f2121f Branched from:25c752a51955337dc61d80a180ed9efa26f2121f (0 newer local commits) Precision:single Parallellization: thread_mpi FFT Library: fftw3 On 04/26/2012 12:07 PM, Carsten Kutzner wrote: On Apr 26, 2012, at 11:37

Re: [gmx-users] GPCR MD Tutorial Using GROMACS (URL)

Hi Anirban: how many ns/day for your simulations? Did you use PME? best Albert On 04/26/2012 12:59 PM, Anirban Ghosh wrote: Hello Albert, Good to know that! I have carried out simulations using this FF in the range of 600 ns. Regards, Anirban -- gmx-users mailing listgmx-users

[gmx-users] blue gene running error

hello: I am running NPT on a blue gene cluster, but the jobs always failed with following messages. However, everything goes well if I run it on my local cluster: ---log--- ol 0.66! imb F 6% pme/F 0.45 step 900, will finish Mon Apr 30 04:46:31 20

Re: [gmx-users] blue gene running error

d any problem with it. But I don't know why it doesn't work in the blue gene computer. THX ALbert On 04/28/2012 07:36 AM, Mark Abraham wrote: On 28/04/2012 2:04 PM, Albert wrote: hello: I am running NPT on a blue gene cluster, but the jobs always failed with following me

Re: [gmx-users] blue gene running error

d any problem with it. But I don't know why it doesn't work in the blue gene computer. THX ALbert On 04/28/2012 07:36 AM, Mark Abraham wrote: On 28/04/2012 2:04 PM, Albert wrote: hello: I am running NPT on a blue gene cluster, but the jobs always failed with following me

[gmx-users] a question about ensemble

hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use semi-isotropy coupling method, which one would be better? thank you very much best Albert -- gmx-users mailing list

Re: [gmx-users] a question about ensemble

Hello Flo: thank you so much for your kind comments. Yes, I would like to couple the pressure, it really helps a lot. best Albert On 05/03/2012 10:40 AM, Dommert Florian wrote: On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods

[gmx-users] how to extract trajectories into individual pdb file?

hello: I've finished a MD job and I am wondering how can we extract individual pdb from trajectories in Gromacs? each time I always get a single pdb contains lots of snapshots. thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromac

Re: [gmx-users] how to extract trajectories into individual pdb file?

On 05/03/2012 05:12 PM, francesco oteri wrote: In particular, look at the option -sep thank you for kind reply. but how to superimposed the left snapshot with the first one? thanks again for helps -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/

Re: [gmx-users] how to extract trajectories into individual pdb file?

thank you very much. I found a problem : there is no option to select step. eg: I would like to export one snapshot at each 10ps, I don't find such kind of options.. THX On 05/03/2012 05:21 PM, francesco oteri wrote: -fit 2012/5/3 Albert mailto:mailmd2...@gmail.com>>

[gmx-users] amber2xtc.py error

hello: I am trying to use amber2xtc.py script to convert Amber MD system into gromacs format by command: python amber2xtc.py npt3.mdcrd apo.prmtop . *.rst md_gromacs however, I got the following messages --log USAGE : python amber2xtc.py AMBERCRD AMBERTOP T

[gmx-users] Fwd: amber2xtc.py error

hello: I am trying to use amber2xtc.py script to convert Amber MD system into gromacs format by command: python amber2xtc.py npt3.mdcrd apo.prmtop . *.rst md_gromacs however, I got the following messages --log USAGE : python amber2xtc.py AMBERCRD AMBERTOP TR

[gmx-users] GPU running problem with GMX-4.6 beta2

hello: I am running GMX-4.6 beta2 GPU work in a 24 CPU core workstation with two GTX590, it stacked there without any output i.e the .xtc file size is always 0 after hours of running. Here is the md.log file I found: Using CUDA 8x8x8 non-bonded kernels Potential shift: LJ r^-12: 0.112 r^-6

Re: [gmx-users] GPU running problem with GMX-4.6 beta2

U setup with -ntomp 12); - try running in GPU emulation mode with the GMX_EMULATE_GPU=1 env. var set (and to match closer the GPU setup with -ntomp 12) - provide a backtrace (using gdb). Cheers, -- Szilárd On Mon, Dec 17, 2012 at 5:37 PM, Albert wrote: hello: I am running GMX-4.6 beta2 GPU wor

Re: [gmx-users] GPU running problem with GMX-4.6 beta2

On 12/17/2012 06:08 PM, Szilárd Páll wrote: Hi, How about GPU emulation or CPU-only runs? Also, please try setting the number of therads to 1 (-ntomp 1). -- Szilárd hello: I am running in GPU emulation mode with the GMX_EMULATE_GPU=1 env. var set (and to match closer the GPU setup with -nt

Re: [gmx-users] GPU running problem with GMX-4.6 beta2

well, that's one of the log files. I've tried both VERSION 4.6-dev-20121004-5d6c49d VERSION 4.6-beta1 VERSION 4.6-beta2 and the latest 5.0 by git. the problems are the same.:-( On 12/17/2012 07:56 PM, Mark Abraham wrote: On Mon, Dec 17, 2012 at 6:01 PM, Albert wrote: >

Re: [gmx-users] GPU running problem with GMX-4.6 beta2

zation and found that there is some problem with my ligand. I regenerated the ligand toplogy with acpype, and resubmit for mimization and NVT. Now it goes well. So probably the problems comes from the incorrect ligand topolgy which make the system very unstable. best Albert -- gmx-users ma

Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers

On 12/20/2012 09:13 AM, pcl wrote: Well what works for me is I convert cgenff and merge it with charmm36 (you only have to do this once per cgenff version), then I have paramchem generate cgenff charges for the ligand. Then I convert the output of paramchem (charges) to .rtp format. I also hav

[gmx-users] voltage for membrane?

ng on this. THX Albert -- 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

[gmx-users] how to convert CGenFF into .itp file?

. This script is trying to generate something like what we see in a complete forcefiled folder instead of a single .itp file for ligand. I am just wondering, how can we convert the output from CGenFF into a single .itp file which is similar to the one from Swissparam? thank you very much best

Re: [gmx-users] how to convert CGenFF into .itp file?

On 12/26/2012 12:18 PM, Peter C. Lai wrote: You don't. CGenFF is a forcefield, like CHARMM36. You install it, add rtp entries then use pdb2gmx to generate a ligand's topology .itp file THX but the problem is how to use this script? I've already download the latest CGenFF file from CHARMM F

Re: [gmx-users] how to convert CGenFF into .itp file?

y has complete necessary information for paramters and topology). Probably one can consider improve this script and export the output file as a single .itp file. best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please se

Re: [gmx-users] how to convert CGenFF into .itp file?

On 12/26/2012 07:53 PM, David van der Spoel wrote: Hey, it's open source. Let us know how it goes you can simple create an account and login https://www.paramchem.org/ after your login, click "upload molecule" in left panel. Now you will see the option: "Include parameters that are already

[gmx-users] how to indicate solvent flexibility?

type Hbonds with resdiues inside protein. I am just wondering how which module of Gromacs can I use to indicate the solvent difference in flexibility? Is it possible to calculate the entropy in certain region (let's say: 20 thank you very much best Albert -- gmx-users mailing list

[gmx-users] g_select error

definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. Assertion failed for "g" in file /home/albert/Desktop/gromacs-4.6-beta3/

Re: [gmx-users] how to indicate solvent flexibility?

file: /home/albert/software/gromacs/src/tools/gmx_msd.c, line: 739 Fatal error: The index group does not consist of whole molecules For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors

Re: [gmx-users] how to indicate solvent flexibility?

On 01/10/2013 11:14 AM, David van der Spoel wrote: On 2013-01-10 10:45, Albert wrote: Hello Justin and Leandro: thanks a lot for kind advices. I am trying to us the g_msd to calculate the density: try g_msd -h wrong tool. that's strange. Here is the information which I think it is

Re: [gmx-users] GROMACS 4.6 release is ready!

How nice it is. Cheers. Albert On 01/21/2013 09:09 AM, Mark Abraham wrote: Hi GROMACS users, The day is finally here - GROMACS 4.6 is out! As you've probably heard by now, there are lots of wonderful new performance features, including * a native GPU implementation layer - thanks to

[gmx-users] question about fftw3 in gromacs 4.6 installation

very much best Albert -- 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 w

Re: [gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric), and topologies to Amber format

probably you can try "catdcd" On 01/21/2013 11:29 AM, Anna Marabotti wrote: Dear gmx-users, I followed the suggestions by Justin and Daniel to convert the trajectories, but still Amber does not recognize the correct format and complains about the fact that it does not find the correct box di

Re: [gmx-users] question about fftw3 in gromacs 4.6 installation

/ for convenience. -Justin Hello Justin: thank you very much for kind comments. It works now. best Albert -- 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

[gmx-users] how can I make statics for Z-axis?

hello: I would like to make statics for an atom along Z-axis. I am just wondering how can I to do this in Gromacs? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

Re: [gmx-users] how can I make statics for Z-axis?

HI Erik: thanks a lot for kind advices, I will try it. best Albert On 01/24/2013 03:00 PM, Erik Marklund wrote: g_traj -nox -noy if I recall correctly. On Jan 21, 2013, at 4:10 PM, Albert wrote: hello: I would like to make statics for an atom along Z-axis. I am just wondering how can I

[gmx-users] make_ndx error

Hello: I am using make_ndx to make a index file in Gromacs 4.6, make_ndx -f input.pdb but it said: Copied index group 1 'Protein' Copied index group 25 'Water_and_ions' One of your groups is not ascending Group is empty thank you very much best Albert -- gmx-users

Re: [gmx-users] make_ndx error

On 01/26/2013 06:53 PM, Justin Lemkul wrote: What exactly did you enter at the make_ndx prompt? -Justin 1|25 protein, water and ions -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs

Re: [gmx-users] make_ndx error

On 01/26/2013 07:41 PM, Justin Lemkul wrote: What types of ions do you have? I can reproduce this problem for a protein with ions bound to it, which are numbered discontinuously with water and ions in solution. -Justin thank you for kind reply. I only have Na+ and Cl-. best Albert

Re: [gmx-users] make_ndx error

On 01/26/2013 07:51 PM, Justin Lemkul wrote: Can you please post the following: 1. The groups printed in the make_ndx prompt 2. The output of gmxcheck on an index file created from your coordinate file (created simply by typing 'q' at the prompt, i.e. not creating any special groups) -Justi

Re: [gmx-users] Using AMBER FF with GROMACS

FF for protein? Currently, there is only CHARMM36 FF for lipids. It seems that the CHARMM36 FF for protein introduced the nbfix term which is absent in any previous version of CHARMM. probably this would take sometime to be introduced to Gromacs. regards Albert -- gmx-users mailing listgmx

[gmx-users] g_membed deprecated?

-stepout 100 Please cite: Wolf et al, J Comp Chem 31 (2010) 2169-2174. does it means that g_membed deprecated from Gromacs-4.6 and we must use mdrun instead? THX Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

Re: [gmx-users] g_membed deprecated?

with errors. not eough space for XTC? However, when I run it in gromacs-4.5.6 by g_membed, it finished well. best Albert -- 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

[gmx-users] problems for GPU simulations

. So I am just wondering what's happening? thank you very much best Albert -- 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

Re: [gmx-users] problems for GPU simulations

On 02/07/2013 11:03 AM, James Starlight wrote: Hi Albert! As I understood your correctly you have run simulations with your 2 GPU cards on Gromacs-beta but could not do it with final version havent it? not really. both versions could run with GPU. The 4.6 beta recognize my number of GPU as 4

Re: [gmx-users] problems for GPU simulations

On 02/07/2013 11:28 AM, James Starlight wrote: Also could you tell me what your system has performance (in gflops) and what system you have simulated on it (average atom number, presence of explicit membrane etc)? it is something around 55,000 atoms with explicit membrane. I am using Slipids F

Re: [gmx-users] problems for GPU simulations

orted | +-+ here is the log for mdrun: Program mdrun_mpi, VERSION 4.6 Source code file: /home/albert/Documents/2013-02-06/gromacs-4.6/src/gmxlib/gmx_detect_hardware.c, line: 356 Fatal error: Incorrect launch configuration: mismat

Re: [gmx-users] problems for GPU simulations

Hi: thanks for kind comments. It works fine now after I recompiled Gromacs carefully. best Albert On 02/08/2013 03:43 AM, Szilárd Páll wrote: Hi, If you have two GTX 590-s four devices should show up in nvidia-smi and mdrun should also show four devices detected. As nvidia-smi shows only

[gmx-users] 4.6 seems improved the efficiency

efficiency 32 ns/day. That's really nice. I don't know whether other users have similar experiences for this new version. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.g

[gmx-users] velocity was not present from trjconv

1.680 3.925 8.606 0.5957 0.0504 -0.4752 1TYRHE1 14 1.728 3.974 8.689 1.1798 -3.6443 1.5406 THX Albert -- 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

Re: [gmx-users] velocity was not present from trjconv

file every 2 ps probably that's the reason why it didn't have velocity informations My md is still running, I am just wondering, is there any way to extract the last snapshot into .gro file with velocity information? thanks best Albert -- gmx-users mailing listgmx-users@g

Re: [gmx-users] velocity was not present from trjconv

Do you have any idea for this? thanks again for kind helps. best Albert -- 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

Re: [gmx-users] velocity was not present from trjconv

. -Justin IC. that's really helpful. thanks a lot Albert -- 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

[gmx-users] can we schedule it?

ering, can specify some parameters in the .mdp file so that Gromacs can export a .gro file with velocity information every 20 ns? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

Re: [gmx-users] GPU version of GROMACS 4.6 in MacOS cluster

The easiest way for solution is to kill MacOS ans switch to Linux. ;-) Albert On 03/01/2013 06:03 PM, Szilárd Páll wrote: Hi George, As I said before, that just means that most probably the GPU driver is not compatible with the CUDA runtime (libcudart) that you installed with the CUDA

Re: [gmx-users] GROMACS 4.6.1 released

Hello: I am wondering did the forcefiled was updated in this new version? eg: did CHARMM36_protein embeded or the CHARMM36_lipids updated? thank you very much Albert On 03/05/2013 08:14 PM, Mark Abraham wrote: *Hi GROMACS users, GROMACS 4.6.1 is officially released. It contains numerous

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