Re: [gmx-users] ERROR: Source code file: statutil.c, line: 727

Dear Uday, What is the command you have given ? Please paste the command lines. sharada -- Original Message -- From: udaya kiran To: gmx-users@gromacs.org Date: Mon, 13 Dec 2010 17:22:07 +0100 Subject: [gmx-users] ERROR: Source code file: statutil.c, line: 727 Dear All, I am unable to carry out t

[gmx-users] Terminal_ARG_residue causing problem in pdb2gmx

Dear Gromacs User My pdb is homodimer with Arg as c-terminal residue. With this pdb I am etting following error in pdb2gmx command Program pdb2gmx, VERSION 4.0.7 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom OXT in residue ARG 107 not found in rtp entry with 17 atoms while

[gmx-users] free energy calculation problem

Hi all, I am using Gromacs4.5 for free energy calculations. At the beginning 6 lambda (0, 0.2, 0.4, 0.6, 0.8, 1.0) are used to test my system. There are two problems: 1. dV/dlambda value at lambda=0.0 is more than 300,000 KJ/mol, which is ten times large than those at the other lambda values

Re: [gmx-users] md.log

Thank you for your help. Rama On Mon, Dec 13, 2010 at 6:39 PM, Itamar Kass wrote: > Hi, > > the log file is not needed for extension. Use something like: > > grompp -f md_extension.mdp -c MD_01.gro -n system.ndx -p system.top -t > MD_01.trr -r MD_01.edr -o MD_02.tpr > > Itamar > > On 14/12/10 1:2

[gmx-users] Coarse-grained simulation with MARTINI

Hello I am trying to perform a CG simulation on the solvated protein but there is one question that I would like to ask for suggestion. The problem is: the volume of the periodic box varied a lot depending on the Van der Waals distance of the CG water molecule. I guess the volume variation is bec

Re: [gmx-users] md.log

Hi, the log file is not needed for extension. Use something like: grompp -f md_extension.mdp -c MD_01.gro -n system.ndx -p system.top -t MD_01.trr -r MD_01.edr -o MD_02.tpr Itamar On 14/12/10 1:29 PM, Ramachandran G wrote: Hi gmx-users: I am trying to extend my simulation run but unfor

Re: [gmx-users] md.log

Ramachandran G wrote: Hi gmx-users: I am trying to extend my simulation run but unfortunately i deleted the file md.log. Is there any way i get my md.log file using the existing .edr or .trr files so that i can proceed further. No. -Justin Thank you. Rama -- =

[gmx-users] md.log

Hi gmx-users: I am trying to extend my simulation run but unfortunately i deleted the file md.log. Is there any way i get my md.log file using the existing .edr or .trr files so that i can proceed further. Thank you. Rama -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.

RE: [gmx-users] mpi run in Gromacs 4.5.3

Thank you, Justin and Mark. I'll recompile gromacs. In my current version -nt is not available (using mdrun -h). Thanks again, JT -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Mon 12/13/2010 5:49 PM To: Discussion list for GROMACS users Subje

Re: [gmx-users] mpi run in Gromacs 4.5.3

On 14/12/2010 11:14 AM, Te, Jerez A., Ph.D. wrote: Hi Mark, Thank you for your reply. Just to confirm, mdrun_mpi is still being used in Gromacs 4.5.3? The gromacs manual (Appendix A.5- Running Gromacs in parallel) suggested using "mdrun -np 8 -s topol -v -N 8" in running a single machine with

Re: [gmx-users] mpi run in Gromacs 4.5.3

Te, Jerez A., Ph.D. wrote: Hi Mark, Thank you for your reply. Just to confirm, mdrun_mpi is still being used in Gromacs 4.5.3? The gromacs manual (Appendix A.5- Running Gromacs in parallel) suggested using "mdrun -np 8 -s topol -v -N 8" in running a single machine with multiple (8) processors

RE: [gmx-users] mpi run in Gromacs 4.5.3

Hi Mark, Thank you for your reply. Just to confirm, mdrun_mpi is still being used in Gromacs 4.5.3? The gromacs manual (Appendix A.5- Running Gromacs in parallel) suggested using "mdrun -np 8 -s topol -v -N 8" in running a single machine with multiple (8) processors and "mpirun -p goofus,doofus

Re: [gmx-users] mpi run in Gromacs 4.5.3

On 14/12/2010 7:48 AM, Te, Jerez A., Ph.D. wrote: Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version of Gromacs. I don't understand what (you think) you mean. You can use thread-based paralleli

Re: [gmx-users] generating new velocities and exploring more of thephase space

Hassan Shallal wrote: Thanks a lot Justin for the valuable feedback about generating different velocities a few days ago... I would like to discuss some analysis questions with the gromacs users, I tried to find solutions to the following points in the literature and/or the mailing list, unf

RE: [gmx-users] generating new velocities and exploring more of thephase space

Thanks a lot Justin for the valuable feedback about generating different velocities a few days ago... I would like to discuss some analysis questions with the gromacs users, I tried to find solutions to the following points in the literature and/or the mailing list, unfortunately, couldn't f

Re: [gmx-users] pathologically expanding box

Greg Bowman wrote: Hello, Has anyone else experienced a pathologically expanding box during equilibration in the NPT ensemble? I've solvated my system with editconf/genbox, energy minimized, equilibrated in NVT with the protein coordinates restrained, and then equilibrated in NPT without a

[gmx-users] Re: pathologically expanding box

Hey, Greg - I believe the problem is more probably located in your GRO file or TOP file rather than in MDP one. Just visualize your structure to check if everything is OK. Also, 50 000 steps can be not enough to get the well-equilibrated configuration. What force and energy is output at the last s

Re: [gmx-users] HBOND probability

Poojari, Chetan wrote: Hello Justin, I commented out line 151 and braces enclosing it. # unless ($resn =~ /SOL/) { for (my $z=1; $z<=$nres; $z++) { if ($donors{$z} == $natom) { $donor_names[$z] = $name; $donor_resn[$z] = joi

RE: [gmx-users] HBOND probability

Hello Justin, I commented out line 151 and braces enclosing it. # unless ($resn =~ /SOL/) { for (my $z=1; $z<=$nres; $z++) { if ($donors{$z} == $natom) { $donor_names[$z] = $name; $donor_resn[$z] = join('', $resn, $resnum);

[gmx-users] Question about COM-Pulling

Dear Chris, thx a lot for your help! Unfortunately, the information you provided is nowhere to be found in the manual. With best wishes, Christian -- for your setup options, the spring potential is something like: U=0.5*k*[(z_ref -

[gmx-users] pathologically expanding box

Hello, Has anyone else experienced a pathologically expanding box during equilibration in the NPT ensemble? I've solvated my system with editconf/genbox, energy minimized, equilibrated in NVT with the protein coordinates restrained, and then equilibrated in NPT without any position restraint

[gmx-users] Question about COM-Pulling

for your setup options, the spring potential is something like: U=0.5*k*[(z_ref - z_pull) - (initial_dist + time*0.01)]^2 (please refer to the manual for more details, I don't do AFM and didn't check the exact functional form). So the spring is not on the displacement but on the difference bet

[gmx-users] mpi run in Gromacs 4.5.3

Hi, I have been trying to run Gromacs 4.5.3 parallel simulations using openmpi 1.4.2. From my understanding, mdrun_mpi is not used in this version of Gromacs. Our system administrator told me that all mpi related options have been turned on while installing Gromacs. With either commands: mdrun -

[gmx-users] Question about COM-Pulling

Here you have time, the z position of your reference group and the difference along z between your pull group and your reference group. There is no "dummy particle" as the spring extends between the "reference" group at z=1.1675 and the "pull" group, which in the first frame is located at z=1

[gmx-users] Re: gmx-users Digest, Vol 80, Issue 90

On 10-12-13 01:29 PM, gmx-users-requ...@gromacs.org wrote: ubject: [gmx-users] Question about COM-Pulling To: MAILINGLIST GROMACS Message-ID:<4d065c09.4020...@rhrk.uni-kl.de> Content-Type: text/plain; charset=UTF-8; format=flowed Hi, although this is not relevant to my previous question: It i

Re: [gmx-users] HBOND probability

Poojari, Chetan wrote: Hello Justin, I commented out the lines from 151-161 # unless ($resn =~ /SOL/) { # for (my $z=1; $z<=$nres; $z++) { #if ($donors{$z} == $natom) { #$donor_names[$z] = $name; #$donor_resn[$z] = join('',

RE: [gmx-users] HBOND probability

Hello Justin, I commented out the lines from 151-161 # unless ($resn =~ /SOL/) { # for (my $z=1; $z<=$nres; $z++) { #if ($donors{$z} == $natom) { #$donor_names[$z] = $name; #$donor_resn[$z] = join('', $resn, $resnum); #

Re: [gmx-users] [Fwd: g_sas for each residu]

> Others alternatives are welcome. Look up NACCESS. It can do what you want on pdb frames extracted from a trajectory. --- On Mon, 12/13/10, Justin A. Lemkul wrote: > From: Justin A. Lemkul > Subject: Re: [gmx-users] [Fwd: g_sas for each residu] > To: "Discussion list for GROMACS users" > Da

Re: [gmx-users] HBOND probability

Poojari, Chetan wrote: Hello Justin, As suggested i did remove the chain identifiers, so i do get residue numbers in my output. But the end result is still the same. While choosing 2 groups to create index file, i choose protein as my first group and sol as my second group. (I choose the ent

[gmx-users] Re: gmx-users Digest, Vol 80, Issue 88

The distance between the com of the pulled group and the dummy particle / spring you have implicit in pullf.xvg (implicit since, it's the distance modified by the force constant of the spring, to get the force). I think the best one can do (to see which are which distances and how they are rel

[gmx-users] Question about COM-Pulling

Hi, although this is not relevant to my previous question: I used mdrun like this: mdrun -v -s pull.tpr -o pull.trr -cpo pull.cpt -c pull.gro -e pull.edr -g pull.log -px pull_dist.xvg -pf pull_force.xvg With an input-file like this: ; Run-Par

RE: [gmx-users] Re: tpbconv extension

No, the point is that in Gromacs version 4.0 (and all versions before) steps were counted in plain int's, which are 32 bit. In version 4.5 they are 64 bit. But I would suggest to upgrade to 4.5.3 for performance reasons. If you can run a microsecond, you are probably running in parallel over many

[gmx-users] Question about COM-Pulling

Dear Christian: As per my original comments, please provide a .mdp file, sample output, and all the other things that I asked for. Chris. --original message-- this is a more general question. I thought that in analogy to an AFM-experiment a "dummy"-particle is placed at a certain distance

Re: [gmx-users] Re: tpbconv extension

Hi Berk, Thanks for the suggestion, does the tpr file generated by the options mention on PC would work on a server with older version of Gromacs i.e. 4.0... Ram On Mon, Dec 13, 2010 at 6:04 PM, Berk Hess wrote: > Sorry, I mistook a million ps for a millisecond, this is a microsecond. > The max

RE: [gmx-users] HBOND probability

Hello Justin, As suggested i did remove the chain identifiers, so i do get residue numbers in my output. But the end result is still the same. While choosing 2 groups to create index file, i choose protein as my first group and sol as my second group. (I choose the entire protein and solvent g

[gmx-users] Question about COM-Pulling

Hi, this is a more general question. I thought that in analogy to an AFM-experiment a "dummy"-particle is placed at a certain distance from the center of mass of the pull group (compare figure 6.1 in the manual). The force is then calculated as the displacement between the pulled atom and the

RE: [gmx-users] Re: tpbconv extension

Sorry, I mistook a million ps for a millisecond, this is a microsecond. The maximum number of steps in version 4.0 is INT_MAX, which is 2,147,483,647. >From the name of your tpr file it seems you are not exceeding this, so I don't know what's wrong exactly. But for this reason (and many other rea

Re: [gmx-users] Re: tpbconv extension

Hi Justin and Berk, Thanks for the suggestions. I am using gromacs 4.0.7 single 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 wrote: > > >

RE: [gmx-users] Re: tpbconv extension

Hi, I fixed the bug for 4.5.4. If you want an unlimited number of steps, use: tpbconv -nsteps -1 Berk From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] Re: tpbconv extension Date: Mon, 13 Dec 2010 17:44:53 +0100 Hi, No this is actually a bug in tpbconv. -nsteps

RE: [gmx-users] Re: tpbconv extension

Hi, No this is actually a bug in tpbconv. -nsteps will not work, because that uses a normal int, not a 64-bit integer. -dt should work, but on line 531 of src/kernel/tpbconv.c (int) should be replaced by (gmx_large_int_t). But are you sure you want to add a millisecond to your simulation time?

[gmx-users] Question about COM-Pulling

The position of the reference group and the displacement of the pulled group from the reference group should be printed (although perhaps without the reference position if you are using absolute coordinate pulling, which is not recommended anyhow). If you want some better advice, please be

Re: [gmx-users] Re: tpbconv extension

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 believe all of

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 wrote: > > > ram bio wrote: >> >> Dear Gromacs users, >> >> I am running a CG simulation for a peptide in lipid bilayer, and the

Re: [gmx-users] Re: tpbconv extension

ram bio wrote: Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulate

[gmx-users] Re: tpbconv extension

Dear Gromacs users, I am running a CG simulation for a peptide in lipid bilayer, and the run didnot extend after 42000 ps using gromacs 4.0.7, Reading toplogy and shit from memb12extnr42000ns.tpr Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) You've simulated long enough. Not

[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 interfa

Re: [gmx-users] ERROR: Source code file: statutil.c, line: 727

udaya kiran wrote: Dear All, I am unable to carry out the md runs due to the following error. /Program grompp, VERSION 4.0.5 Source code file: statutil.c, line: 727 Invalid command line argument: / which is further followed by /Program mdrun, VERSION 4.0.5 Source code file: gmxfio.c, line

[gmx-users] ERROR: Source code file: statutil.c, line: 727

Dear All, I am unable to carry out the md runs due to the following error. *Program grompp, VERSION 4.0.5 Source code file: statutil.c, line: 727 Invalid command line argument: * which is further followed by *Program mdrun, VERSION 4.0.5 Source code file: gmxfio.c, line: 736 Can not open fil

Re: [gmx-users] Not have PDB file of peptide

swati shah wrote: Hello Gromacs Users, If I don't have PDB file of any peptide then how can I start the simulation in Gromacs? Does Gromacs has any other way to convert peptide into Gromacs file(.gro file) ? Strictly speaking, a .gro file is not required; almost any coordinate file form

[gmx-users] Not have PDB file of peptide

Hello Gromacs Users, If I don't have PDB file of any peptide then how  can I start the simulation in Gromacs? Does Gromacs has any other way to convert peptide into Gromacs file(.gro file) ? Please help me out. -Swati -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/m

[gmx-users] Question about COM-Pulling

Dear users, I've got a short question regarding com-pulling. From what I understand Umbrella pulling is the same as AFM pulling using a harmonic potential. Why is the position of the spring in the pullx.xvg not printed? One can only find the vector between both pull groups. I looked into olde

RE: [gmx-users] problem building Gromacs 4.5.3 using the Intel compiler

Hi, thanks for the advice. You were spot on: the FFTW library was compiled using PGI and Gromacs using Intel, so I have re-compiled FFTW using Intel and it all works now. Thanks ever so much people! From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark

Re: [gmx-users] problem building Gromacs 4.5.3 using the Intel compiler

Hi, you might also need to use the mpiicc compiler wrapper instead of the mpicc to enforce using icc instead of gcc. Carsten On Dec 13, 2010, at 2:20 PM, Mark Abraham wrote: > > > On 12/13/10, "Miah Wadud Dr (ITCS)" wrote: >> Hello, >> >> I am trying to build Gromacs 4.5.3 using the Intel c

Re: [gmx-users] problem building Gromacs 4.5.3 using the Intel compiler

On 12/13/10, "Miah Wadud Dr (ITCS)" wrote: > Hello, > > I am trying to build Gromacs 4.5.3 using the Intel compiler, but I am > encountering the following problems when I type "make": > It seems like there's some mismatch between how FFTW was compiled and how you're linking to it. Try a fr

Re: [gmx-users] [Fwd: g_sas for each residu]

On 12/13/10, Stephane Abel wrote: > Hi all, > > > I would like to use g_sas to compute and give surface area changes of each > residu of a peptide (25 AA long) and *not* the average per residu given by > the argument -or) along the simulation time. If yes how ?  Of course, i > think, i can

[gmx-users] problem building Gromacs 4.5.3 using the Intel compiler

Hello, I am trying to build Gromacs 4.5.3 using the Intel compiler, but I am encountering the following problems when I type "make": /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 -tpp7 -axW -ip -w -msse2 -funroll-all-loops -std=gnu99 -L/gpfs/grace/fftw-3.2.2/lib -o grompp grompp.o

Re: [gmx-users] [Fwd: g_sas for each residu]

Stephane Abel wrote: Hi all, I would like to use g_sas to compute and give surface area changes of each residu of a peptide (25 AA long) and *not* the average per residu given by the argument -or) along the simulation time. If yes how ? Of course, i think, i can use an index file, but for

Re: [gmx-users] HBOND probability

Poojari, Chetan wrote: Hello Justin, I wanted to find the probability of hydrogen bond formed between my peptide and water molecules over time. So I used your plot_hbmap.pl script. As mentioned in the script file, my index file contained atom numbers only from the [hbonds...] section, rest

[gmx-users] [Fwd: g_sas for each residu]

Hi all, I would like to use g_sas to compute and give surface area changes of each residu of a peptide (25 AA long) and *not* the average per residu given by the argument -or) along the simulation time. If yes how ? Of course, i think, i can use an index file, but for 25 AA, it will take a

Re: [gmx-users] perl script for g_hbond

Olga Ivchenko wrote: Dear Justin, I ran you H bond frequency script and I got the following result. I am understanding that the occupancy of H bonds is on the writeside, but somehow in donor and acceptor column there is the residue name not atom type. I am not quiet good iunderstanding my o

Re: [gmx-users] Re: g_energy: Energy names magic number mismatch

Mikhail Stukan wrote: Justin, Thanks a lot. Concatenation seems to be the only solution, but it works fine. It look like there are some problems with the appending routine on BlueGene. Please file a bugzilla so this issue gets fixed. -Justin Mikhail Dear Justin and Berk, Thank you ve

[gmx-users] HBOND probability

Hello Justin, I wanted to find the probability of hydrogen bond formed between my peptide and water molecules over time. So I used your plot_hbmap.pl script. As mentioned in the script file, my index file contained atom numbers only from the [hbonds...] section, rest were deleted. Heres my sh

Re: [gmx-users] perl script for g_hbond

Dear Justin, I ran you H bond frequency script and I got the following result. I am understanding that the occupancy of H bonds is on the writeside, but somehow in donor and acceptor column there is the residue name not atom type. I am not quiet good iunderstanding my output. Please can you advice

[gmx-users] Re: g_energy: Energy names magic number mismatch

Justin, Thanks a lot. Concatenation seems to be the only solution, but it works fine. It look like there are some problems with the appending routine on BlueGene. Mikhail > Dear Justin and Berk, > > Thank you very much for the hint. Unfortunately, upgrade to 4.5.3 version > doesn't solve the p