[gmx-users] Ca ion simulation incorporated in protein structure

Dear Gromacs Users, I am trying to simulate a modeled protein -ligand complex in lipid bilayer using Gromacs 4.5.4 with Charmm27 FF. For my project purpose which is to see the effect of substitution of ions (Ca instead of Na ions) in the protein structure on protein ligand interactions , I have

[gmx-users] xmgrace graphs

Dear Gromacs users, I am trying to find inter atomic distances between ligand atoms and protein residues using Gromacs commands and could generate individual xvg files, but could not figure out how to merge or show all the xvg files in one graph using xmgrace. Cold you please suggest? Thanks

Re: [gmx-users] xmgrace graphs

. Distance plots produced by g_dist have four data sets (distance and x,y,z components) so plotting in this way can be quite messy. Leave out the -nxy if you want to only plot the total distance and not the remaining (x,y,z) components. -Justin On Tue, Oct 2, 2012 at 8:49 PM, ram bio rmbio

[gmx-users] barium ion simulation

Dear Gromacs Users, I am trying to simulate a protein in lipid bilayer with a barium ion binding pocket in it, with Charmm27 FF in gromacs 4.5.4. I found that barium ion is not included under charmm27 ff ions.itp. I was wondering if there is any way to simulate protein with barium bound using

[gmx-users] Occupancy for a distance cut off

Dear Gromacs Users, I have a run a MD simulation on protein bound with ligand and ions using Gromacs 4.5.4. I am able to calculate the distances between ions and coordinating residues using g_dist. The output is in the form of xvg file, but I am looking for the occupancy for a cut off distance

Re: [gmx-users] Occupancy for a distance cut off

, Justin Lemkul jalem...@vt.edu wrote: On 2/11/13 6:15 PM, ram bio wrote: Dear Gromacs Users, I have a run a MD simulation on protein bound with ligand and ions using Gromacs 4.5.4. I am able to calculate the distances between ions and coordinating residues using g_dist. The output

Re: [gmx-users] Occupancy for a distance cut off

Thank you!! On Mon, Feb 11, 2013 at 8:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/11/13 9:16 PM, ram bio wrote: Hi Justin, Thanks for the suggestion. I executed the following command: g_dist -f n101c2naclprod2-12nsvrpr.trr -s n101c2naclpose2prod2nsvrpr.tpr -n index.ndx -dist 0.35

[gmx-users] Energetics of ion and subatrate binding sites

Dear Gromacs Users, I have simulated a protein with different ions and same substrate bound to it in POPC lipid bilayer using Groamcs 4.5.4. The ion binding and substrate binding sites are coupled. After Md simulation we see a reorganization of these sites. Now, we are trying to calculate the

[gmx-users] POPC bilayer with Charmmff

Dear Gromacs users, I have downloaded the POPC bilayer molecular coordinates with charmmff equilibrated from Dr. Klauda's website. In this site it is mentioned Note: If you run these simulations in NAMD you MUST use NAMD 2.7b3 with vdw ForceSwitching turned on; what does vdw ForceSwitching

[gmx-users] unknown cmap torsion between atoms

Dear Gromacs users, I have built a protein embedded in popc bilayer and executed pdb2gmx using charmm27 ff on the system and the toplogy file was created without errors, but when wanted to minimise the system with grompp i am getting an error as : unknown cmap torsion between atoms 8377 8379 8381

Re: [gmx-users] unknown cmap torsion between atoms

/2011 1:24 PM, ram bio wrote: Dear Gromacs users, I have built a protein embedded in popc bilayer and executed pdb2gmx using charmm27 ff on the system and the toplogy file was created without errors, but when wanted to minimise the system with grompp i am getting an error as : unknown cmap

[gmx-users] charmm 27 gromacs version mdp query

Dear Gromacs Users, I have a protein lipid bilayer system built using Gromacs 4.5.4 and charmm27 FF. Now, i want to equilibrate the built in system using NPT ensemble, for that i have made to mdp files and as i have never used Charmm, I am not sure whether the mdp files i am using are correct, so

[gmx-users] charmm 27 FF mdp query

Dear Gromacs Users, I have a protein lipid bilayer system built using Gromacs 4.5.4 and charmm27 FF. Now, i want to equilibrate the built in system using NPT ensemble, for that i have made to mdp files and as i have never used Charmm, I am not sure whether the mdp files i am using are correct, so

[gmx-users] grompp segmentation error

Dear Gromacs Users, Iam following Drug/Enzyme complex solvation tutorial by John E. Kerrigan, I am unable to execute the grompp step as per the tutorial, the output of grompp command is as follows: grompp -f minim.mdp -c trp_b4ion.gro -p trp.top -o trp_b4ion.tpr

Re: [gmx-users] grompp segmentation error

and help me. Thanks, Ram On Thu, Dec 31, 2009 at 11:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, Iam following Drug/Enzyme complex solvation tutorial by John E. Kerrigan, I am unable to execute the grompp step as per the tutorial, the output

Re: [gmx-users] grompp segmentation error

Mon Aug 24 08:21:56 EDT 2009 compilers: C and fortran Intel 10.1 Please suggest me as the grompp command also donot work with this configuration. Thanks, Ram On Mon, Jan 4, 2010 at 6:17 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the response. I am

Re: [gmx-users] grompp segmentation error

: ram bio wrote: Dear Justin, Thanks for the response. Here is the info regarding the cluster where gromacs version 4.0.5 is installed with icc compliers.  $ ./configure --prefix=/usr/local/gromacs --enable-mpi --with-fft=fftw2 uname -m = x86_64 uname -r = 2.6.18-128.7.1.el5 uname -s

[gmx-users] Multiprotein lipid bilayer

Dear Gromacs Users, I would like to run molecular dynamics by inserting multiple proteins in the same lipid bilayer using gromacs, is it possible? if so, please let me know if any tutorial is available or any kind of help is available Thanks in advance, Ram -- gmx-users mailing list

Re: [gmx-users] Multiprotein lipid bilayer

know the other ways to insert the proteins in lipid bilayers Ram On Thu, Mar 4, 2010 at 4:36 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I would like to run molecular dynamics by inserting multiple proteins in the same lipid bilayer using gromacs

Re: [gmx-users] Multiprotein lipid bilayer

hi justin, will try that thanks Ram On Thu, Mar 4, 2010 at 4:51 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: HI Justin, Thanks for the info. I have followed your tutorial earlier, it really works, and that was for 1 protein, but if 2 or more different kinds

[gmx-users] conversion of desmond trajectory files into gromacs

Dear All, I have run a dynamics of protein ligand complex in lipid bilayer dppc using desmond software and would like to convert the trajectory files files into gromacs format, is it possible?? if so, please let me know your suggestions. Thanks, Ram -- gmx-users mailing list

Re: [gmx-users] conversion of desmond trajectory files into gromacs

Thanks Xavier, Could you make it more eloborate... Ram On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole x.peri...@rug.nl wrote: VMD reads Desmond trajectories and writes GMX format ... Rests the topology to deal with ... On Apr 16, 2010, at 4:15 PM, ram bio wrote: Dear All, I have run

[gmx-users] coarse grain dynamics

Dear Gromacs Users, I have done coarse grain simulation for 2 peptides in bilayer for 1000ns, and now i would like to know the hydrogen bond interactions between these two peptides. Please let me know how to do this, i can visualize the trajectory in VMD, but unable to calculate the hydrogen

Re: [gmx-users] coarse grain dynamics

need to know the hydrogen bond interactions you need to do some all atoms simulation, not coarse grain. Nuno Azoia On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote: Dear Gromacs Users, I have done coarse grain simulation for 2 peptides in bilayer for 1000ns, and now i would like

Re: [gmx-users] coarse grain dynamics

likely NOT be able to draw conclusions from it. Otherwise, everyone would run really fast simulations in CG, then reconstruct their systems afterward. :) Quoting Justin A. Lemkul jalem...@vt.edu: ram bio wrote: thanks, but i am using gromacs version 4.0.07 I think the general

Re: [gmx-users] coarse grain dynamics

thanks all for the discussion. On Tue, May 25, 2010 at 5:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Thanks for the comments and info, but is there any way to take a particular  frame for eg. the last frame  of CG simulation and extend the run into all-atom simulation

Re: [gmx-users] RHEL OS, g_mdrun

it is difficult now to figure out why I could not use g_mdrun_openmpi, even though the file exists in the path:/usr/lib64/openmpi/bin/g_mdrun_openmpi Ram On Wed, May 18, 2011 at 3:00 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I am trying to run a gromacs

[gmx-users] make_ndx unable to save

Dear Gromacs Users, I have simulated a protein -ligand complex in the popc bilayer and while analysing the results i want to find distance between two residues in the protein during simulation. For that I think I have to use g_hbond command by creating an index.file containing the new groups,

[gmx-users] mktop

Dear Gromacs Users, I am using opls FF for my protein-ligand simulations in lipid bilayer. I have generated the topologies for the ligand using MKtop. The output from the MKTOP gives the top file, but not the coordinate/structure file. Please let me know if any tutorial is available for merging

Fwd: [gmx-users] mktop

I have attached the topol.top, ligand.itp files for your information, Please let me know your suggestions to fix this error. Thanks, Pramod On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I am using opls FF for my protein

Re: [gmx-users] mktop

A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the information. Initially, i just wanted to run a simulation of protein-ligand in water solvent . I renamed the topology.top generated from mktop to ligand.itp; and included the ligand.itp line in the topol.top file

Re: [gmx-users] mktop

simulations. Thanks in advance, Pramod On Wed, Oct 12, 2011 at 3:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As i generated the protein-ligand docked complex using opls FF, for the consistency, i am trying to use opls ff generated ligand parameters during

Re: [gmx-users] mktop/swissparam

for gromacs MD simulations. Thanks in advance, Pramod On Wed, Oct 12, 2011 at 3:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As i generated the protein-ligand docked complex using opls FF, for the consistency, i am trying to use opls ff generated ligand

Re: [gmx-users] mktop

structure for embedding the protein and use the related CHARMM FF parameterised itp in the topology file in gromacs for MD simulation. Thanks in advance, Pramod On Wed, Oct 12, 2011 at 7:51 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks, and I accept your

[gmx-users] pdb2gmx charmm topology lipid

On Wed, Oct 12, 2011 at 8:21 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks. The POPC bilayer i am using is with berger lipids, corrected for dihedrals so as to be compatible with the OPLS FF for aminoacids. I think significantly more parameters than just

[gmx-users] inversion of lipid bilayer with water in the centre

Dear Gromacs Users, I have a lipid bilayer with me and I would like to simulate a system by keeping the water molecules with proteins in it and lipid surrounding the water on both sides, can any body suggest me please... Thanks Ram -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] trjcat : Magic Number Error in XTC file (read 0, should be 1995)

Subject: trjcat : Magic Number Error in XTC file (read 0, should be 1995) Dear Gromacs Users, I am trying to cat the .xtc files using the trjcat option in gromacs, but i am getting an error Program gmxcheck, VERSION 4.0.7 Source code file: xtcio.c, line: 85 Fatal error: Magic Number Error in

[gmx-users] swiss param query,

Dear Gromacs Users, I have generated the topology and parameters files for my ligand through swiss param site. Now i am trying to run a simulation of protein ligand complex in POPC bilayer using OPLS force field in Gromacs, but when I am using the grompp command in gromacs for tpr generation I am

[gmx-users] Inflategro

Dear Gromacs Users, While I was runing the Justin's tutorial that is KALP-15 in DPPC , I have some queries regarding the INFLATEGRO, Please have patience to read and answer my queries: 1) does the system.gro should include the position restrained file of KALP_newbox.gro after running genrestr,

[gmx-users] nvt.gro

Dear Gromacs Users, I am following the justin tutorial on KALP-15 in lipid bilayer, I have a query regarding the nvt.gro that is after the NVT equillibration phase. The mdrun was proper without any warnings or errors, but when i visuallized the nvt.gro in VMD, i found that the peptide is intact

Re: [gmx-users] nvt.gro

Dear Justin, Thanks for the suggestion, will try to apply position restraints on lipid as mentioned in the advanced trouble shooting section. Ram On Tue, Sep 22, 2009 at 8:08 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I am following the justin

Re: [gmx-users] nvt.gro

suggest me what to do to lower the gap after NVT equillibration even after applying the lipid restraints and is it ok for my NPT equillibration as there are no gaps between the layers after this NPT equillibration. Thanks Ram On Tue, Sep 22, 2009 at 8:25 PM, ram bio rmbio...@gmail.com wrote: Dear

Re: [gmx-users] nvt.gro

suggest, is it the right way i am following..as i will be not be using NVT equillibration anywhere through out the process. Thanks, Ram On Fri, Sep 25, 2009 at 11:23 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As suggested, i increased the force constant in the Z

Re: [gmx-users] nvt.gro

Dear Justin, Thanks for the options and suggestions, will be back after some trials with modelled proteins. Ram On Mon, Sep 28, 2009 at 6:17 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, When I used the energy mininized system for NPT annealing with position

[gmx-users] neutralizing membrane protein in lipid bilayer +water

Dear Gromacs users, I have a modelled protein whose net charge is +12.69, and I would like to ionize the protein to make it neutral using genion command, but in genion command we can add a specific number of postive or negative charged ions which for my case would not completely neutralize the

Re: [gmx-users] neutralizing membrane protein in lipid bilayer +water

in pdb file (4815) are not matching even though the number of residues are matching after pdb2gmx step. Thanks, Ram and selected choose the Gromos96 53a6 parameter and none options On Tue, Sep 29, 2009 at 7:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs

Re: [gmx-users] neutralizing membrane protein in lipid bilayer +water

, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, Thanks Justin and Marc for the response and you were right. As suggested, i had a view in the modelled protein pdb file and here both the terimus are capped that is as follows; ATOM 1 N THR A 62

Re: [gmx-users] neutralizing membrane protein in lipid bilayer +water

proteins. Thanks Ram On Tue, Sep 29, 2009 at 10:16 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks and as per suggestion, now i have corrected the original modelled pdb file and executed the pdb2gmx command with n-terminus option 1 (NH2) and C-terminus

Re: [gmx-users] neutralizing membrane protein in lipid bilayer +water

Dear Justin, Thanks for the suggestions and will be back after sometime after following the trials. Ram On Tue, Sep 29, 2009 at 10:45 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, I was trying to model a part of the protein involved in the active site

Re: [gmx-users] 256 DPPC bilayer

Dear Justin, Thanks. Ram On Mon, Oct 5, 2009 at 7:30 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I am looking for a DPPC bilayer system of 256 and above , can anybody suugest me the site from where I can download Please... Take a pre-equilibrated 128

[gmx-users] step 0Segmentation fault

Dear Gromacs Users, I have inserted the protein in lipid bilayer and performed Inflategro I am able to reach the required area per lipid after certain iterations but was unable to get the standard Epot and Fmax values that is negative and to the power of 5 or 6 and Fmax less than 1000 during the

Re: [gmx-users] step 0Segmentation fault

.Temperature Pressure (bar) Cons. rmsd () 3.08099e+172.31982e+151.01551e+167.25066e+04 Please diagnose the information and suggest. Thanks ram On Tue, Oct 6, 2009 at 4:12 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I have inserted

Re: [gmx-users] step 0Segmentation fault

and position it in the bilayer and redo the inflategro procedure. Thanks Ram On Tue, Oct 6, 2009 at 4:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the advice. I am using the DPPC 128 lipid bilayer from D. Peter Tieleman website, and the nvt.mdp

Re: [gmx-users] step 0Segmentation fault

. Thanks, Ram On Tue, Oct 6, 2009 at 5:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As suggested, when i reexamined the system.gro (protein_newbox + dppc128) one of the ends of the problem (as i think) i.e. few aminoacids of protein were beyond the water surface

[gmx-users] Gromacs installation on the cluster

Dear Gromacs Users, About Gromacs installation on the cluster, we compiled it on both the login node and the computing nodes. I'd like to know which gromacs programs can be run on the login node without disturbing all other users and which ones must be run on the computing nodes (e.g. the MD

[gmx-users] Error during NVT equillibration

Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized in every step.Then,

[gmx-users] Error during NVT equillibration with nvt.log file

Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized in every step.Then,

Re: [gmx-users] Error during NVT equillibration with nvt.log file

: ram bio wrote: Dear Gromacs users, I am doing protein in lipid-bilayer simulation and i am following the procedure as per justin tutorial. I am able to insert the protein in lipid bilayer and minimize the system as per Inflategro procedure,during the total procedure the system was minimized

Re: [gmx-users] Error during NVT equillibration with nvt.log file

: grompp -f npt.mdp -c anneal_npt1.gro -t anneal_npt.trr -p topol.top -n index.ndx -o npt.tpr Thanks, Ram On Fri, Oct 16, 2009 at 10:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks and I tried your suggestion, that is minimizing the system without

Re: [gmx-users] Error during NVT equillibration with nvt.log file

, 2009 at 7:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: snip Now as i would like to proceed further, please suggest me how to confirm that the simulated annealing was proper and also please let me know can i now go to npt equillibration using the output of simulated annealing

Re: [gmx-users] Error during NVT equillibration with nvt.log file

wrote: ram bio wrote: Dear Justion, When I executed the command g_energy -f anneal_npt1.edr, the output for temperature and pressure were as under: Statistics over 51 steps [ 0. thru 500. ps ], 1 data sets All averages are exact over 51 steps Energy

Re: [gmx-users] Error during NVT equillibration with nvt.log file

Dear Justin, Thanks, will be back after some trials. Ram On Tue, Oct 20, 2009 at 8:16 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the advice and suggestions, will look into the plots and try to run a further NPT equillibration, (here you mean

[gmx-users] Protein Solvent Dynamics - Coordinates for docking

Dear Gromacs Users, I have performed a protein in solvent simulation for 1 ns, the got the output files as: md_0_1.cpt md_0_1.edr md_0_1.gro md_0_1.log md_0_1.tpr md_0_1.trr md_0_1.xtc. I am following Justin Tutorial. Can anybody tell me how to extract the coordinates ? of the simulated

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

, Ram On Wed, Oct 21, 2009 at 4:42 PM, Mark Abraham mark.abra...@anu.edu.au wrote: ram bio wrote: Dear Gromacs Users, I have performed a protein in solvent simulation for 1 ns, the got the output files as: md_0_1.cpt md_0_1.edr md_0_1.gro md_0_1.log md_0_1.tpr md_0_1.trr md_0_1.xtc

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

jalem...@vt.edu wrote: ram bio wrote: Dear Mark, Thanks for the advice and suggestions. I have used trjconv command as in the justin tutorial (trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact), but when i loaded the md_0_1.gro followed by md_0_1_noPBC.xtc in VMD

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

to retrieve the lowest energy configuration is correct. Thanks, Ram On Wed, Oct 21, 2009 at 7:37 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, Thanks for the suggestion and advice. As i have used a modelled protein and want to obtain the lowest energy

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

Dear Mark, You mean that I should consider a configuration with the lowest total energy for docking studies..Please clarify and suggest me. Thanks, Ram On Thu, Oct 22, 2009 at 3:56 AM, Mark Abraham mark.abra...@anu.edu.au wrote: ram bio wrote: Dear Justin, Thanks for the suggestion

Re: [gmx-users] Protein Solvent Dynamics - Coordinates for docking

that can be the input for flexible docking. Thanks, Ram On Thu, Oct 22, 2009 at 4:59 PM, Mark Abraham mark.abra...@anu.edu.au wrote: ram bio wrote: Dear Mark, You mean that I should consider a configuration with the lowest total energy for docking studies..Please clarify and suggest me

Re: [gmx-users] Error during NVT equillibration with nvt.log file

SOL_CL- Thanks, Ram On Tue, Oct 20, 2009 at 7:59 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justion, When I executed the command g_energy -f anneal_npt1.edr, the output for temperature and pressure were as under: Statistics over 51 steps [ 0. thru 500. ps

Re: [gmx-users] Error during NVT equillibration with nvt.log file

Dear Justin, Thanks for your patience and suggestions, as I am new to gromacs, i had to confirm my results. Ram On Mon, Oct 26, 2009 at 4:28 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As per the suggestions, I have run NPT equillibration (without constraints

Re: [gmx-users] Truncation of file traj.trr failed

for 20 ns and the output is md20.tpr) or can i use the same tpr file (md20.tpr) or i require to change the command to continue.. Please help. Thanks, Ram On Fri, Nov 6, 2009 at 10:15 PM, ram bio rmbio...@gmail.com wrote: Dear Justin, Thanks for the information regarding the bug, will try

Re: [gmx-users] Truncation of file traj.trr failed

A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Justin, As per the suggestions in the bug, i changed the line in src/gmxlib/checkpoint.c file on the cluster: from outputfiles[i].offset = ( ((off_t) offset_high) 32 )| ( (off_t) offset_low ); to outputfiles[i].offset = ( ((off_t

[gmx-users] tpbconv extension

Dear Gromacs users, I -- 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] Re: tpbconv extension

. Not writing tpr file Please give your suggestions to overcome this error. Ram On Mon, Dec 13, 2010 at 5:26 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] Re: tpbconv extension

Hi Justin, The command was: tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr Thanks Ram On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer

Re: [gmx-users] Re: tpbconv extension

...@vt.edu wrote: ram bio wrote: Hi Justin, The command was: tpbconv -s memb12extnr42000ns.tpr -extend 100 -o memb12extnr43000ns.tpr Try using -nsteps instead.  There are issues with -extend and -until (bad rounding, limits to the size of the number, etc) that can cause this problem.  I

Re: [gmx-users] Re: tpbconv extension

precision, and would like to extend my run each time by 1 microsec as it fits into the wall time on the server for my system. Please suggest. Thanks Ram On Mon, Dec 13, 2010 at 5:40 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Hi Justin, The command

[gmx-users] cannot rename checkpoint file

Dear Gromacs users, I am running an all-atom simulation of protein-ligand complex in lipid bilayer on a server, while running the job after some time, my job terminates with an error as under: Program mdrun, VERSION 4.0.3 Source code file: checkpoint.c, line: 859 File input/output error:

[gmx-users] protein movement in lipid bilayer during simulation

Dear Gromacs Users, I am performing an all-atom simulation of protein ligand complex in lipid bilayer , but after around 100ns, I see that the protein started moving in one dimension in the lipid bilayer that is it is not in the centre, I want the position of the protein fixed through out the

Re: [gmx-users] protein movement in lipid bilayer during simulation

Dear Justin, Thanks for the suggestion. Best, Ram On Thu, Jan 27, 2011 at 6:46 PM, Justin A. Lemkul jalem...@vt.edu wrote: ram bio wrote: Dear Gromacs Users, I am performing an all-atom simulation of protein ligand complex in lipid bilayer , but after around 100ns, I see