[gmx-users] parallel mdrun

2009-09-17 Thread Jarol E. Molina
Hi all I have a single machine with multilpe processors. I want run mdrun with 8 processors and I use the options % mdrun – np 8 -s toppl.tpr -v -N 8 I see in the system monitor that just one procesor is running, if I use %mdrun_mpi -np 8 -s topol.tpr -v -N 8 I see the same in the system

[gmx-users] msd not linear and c.o.m removal

2009-09-17 Thread Jennifer Williams
Hi, I am running simulations of gaseous molecules (CH4, C2H6, CO2, N2) in a silica pore (4nm in diameter), cell dimensions, 46 x 44 x 37. This in an infinite pore in the z direction. I am interested in looking at diffusion but I am a bit concerned about the shape of my MSD curves, for a 5

[gmx-users] Another problem with DNA

2009-09-17 Thread Gunnar Widtfeldt Reginsson
I am trying to run grompp using a pdb file of DNA duplex, a sucessfully generated topology, and the steep.mpd from http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top I am getting the fatal error: Fatal error: [ file spc.itp, line 37 ]: Atom index (1) in bonds out of bounds (1-0). Th

[gmx-users] 3 covalent bonds protein- heme

2009-09-17 Thread malvezzi
Dear Friends, I have to make three covalent bonds between the protein and the heme group. I have parameters for heme and the residues. Do I have to make as if everything belongs to the same molecule? (as it realy is) Has anyone done something like this? Thanks Alberto

[gmx-users] about intermolecular interactions

2009-09-17 Thread wuxiao
Dear GMXers, For long time, I have had a puzzle: while the top file generally describe interactions in a molecule, intermolecular interactions are not explicitly in the top file. How are these intermolecular interactions described in GROMACS? Thanks a lot for any reply. Sincerely, C

Re: [gmx-users] Large fluctuation of protein temperature with nose hoover thermostat

2009-09-17 Thread Omer Markovitch
The group PROTEIN isn't very large as the group NONPROTEIN, therefore its total kinetic energy fluctuates more. --Omer. On Wed, Sep 16, 2009 at 12:10, Stephane Abel wrote: > tc-grps = Protein Non-Protein ; two coupling groups - more accurate > tau_t = 0.4 0.4 ; time constant, in ps > ref_t = 310

Re: [gmx-users] about intermolecular interactions

2009-09-17 Thread Justin A. Lemkul
wuxiao wrote: Dear GMXers, For long time, I have had a puzzle: while the top file generally describe interactions in a molecule, intermolecular interactions are not explicitly in the top file. How are these intermolecular interactions described in GROMACS? Thanks a lot for any reply. S

Re: [gmx-users] parallel mdrun

2009-09-17 Thread Justin A. Lemkul
Jarol E. Molina wrote: Hi all I have a single machine with multilpe processors. I want run mdrun with 8 processors and I use the options % mdrun – np 8 -s toppl.tpr -v -N 8 I see in the system monitor that just one procesor is running, if I use %mdrun_mpi -np 8 -s topol.tpr -v -N 8 I see

[gmx-users] [Fwd: free energy calculation]

2009-09-17 Thread David van der Spoel
Original Message Subject:free energy calculation Date: Wed, 16 Sep 2009 11:34:25 -0400 From: Elio Cino To: sp...@gromacs.org Hello. Dr. van der Spoel. I have been waiting for an account to be made on gmx-users so that i can post. Until the account is made, I

[gmx-users] Generating initial coordinates and velocities from scratch.

2009-09-17 Thread Lum Ngwagia
Hello everyone,    I have been struggling to find a way to supply initial coordinates and initial velocities to a molecule like pentane. I want to add about 2500 molecules of pentane to a box, but all these molecules must have initial positions and velocities. I have used ghemical to draw t

[gmx-users] Periodic Boundary Conditions & Location of Atoms Near Box Edges

2009-09-17 Thread Darrell Koskinen
Dear GROMACS Gurus, In order to correctly model an infinite graphene sheet using periodic boundary conditions, should the box edges be located at the midpoints between the atomic bonds? Thanks. Darrell ___ gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] Another problem with DNA

2009-09-17 Thread Justin A. Lemkul
Gunnar Widtfeldt Reginsson wrote: I am trying to run grompp using a pdb file of DNA duplex, a sucessfully generated topology, and the steep.mpd from http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top I am getting the fatal error: Fatal error: [ file spc.itp, line 37 ]: Atom i

Re: [gmx-users] parallel mdrun

2009-09-17 Thread Sander Pronk
You need to run MPI jobs with 'mpirun'. The correct command would be mpirun -np 8 mdrun -s topol.tpr (I don't know what the -N 8 does). Sander On 16 Sep 2009, at 18:03 , Jarol E. Molina wrote: Hi all I have a single machine with multilpe processors. I want run mdrun with 8 processors and

Re: [gmx-users] Another problem with DNA

2009-09-17 Thread Mark Abraham
Gunnar Widtfeldt Reginsson wrote: I am trying to run grompp using a pdb file of DNA duplex, a sucessfully generated topology, and the steep.mpd from http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/build.html#top I am getting the fatal error: Fatal error: [ file spc.itp, line 37 ]: Atom ind

[gmx-users] Unit of RMSD of g_energy -f -f2

2009-09-17 Thread Ragnarok sdf
Is the RMSD given by g_energy -f -f2 in Joule or KJoule? ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (

Re: [gmx-users] pdb2gmx with amber99 can't find an atom in a DNA duplex

2009-09-17 Thread Gunnar Widtfeldt Reginsson
Problem is solved. The atom needed to be called O not O2. Thanks, On Tue, Sep 15, 2009 at 11:29 PM, Justin A. Lemkul wrote: > > > Gunnar Widtfeldt Reginsson wrote: > >> Hi. Can someone please help me. >> >> I am new to Gromacs. I have a 20mer DNA duplex I want to do some MD on. I >> start by mak

Re: [gmx-users] compiling problem

2009-09-17 Thread Yang Ye
Just a work-around, force mpicc to point to cc. alias mpicc=cc Yang Ye On Wed, Sep 16, 2009 at 5:35 PM, Mu Yuguang (Dr) wrote: > No, even I do not use mpi , the error is still there. > > > > Regards > > Yuguang > > > -- > > *From:* gmx-users-boun...@gromacs.org [m

Re: [gmx-users] Core i7 vs Core2Quad

2009-09-17 Thread Sander Pronk
Hi, In Linux, one can apparently set processor affinity (or, in this case core affinity) with 'taskset'. The command is used like this: taskset command where is a hexadecimal bit mask with the cpus to use (in a format like 0xff, where 0xff enables the first 8 cpus on a system). For mdr

Re: [gmx-users] some questions about the tabulated interaction functions

2009-09-17 Thread Mark Abraham
wuxiao wrote: > Dear GMXers, >by looking through the manual, I find that the tabluated interaction > functions seem very flexible for performing MD simulations. But some > questions puzzle me too much: > for bonded interactions, as for bonds, angles, dihedrals, the f'(x) > are the derivati

Re: [gmx-users] Generating initial coordinates and velocities from scratch.

2009-09-17 Thread Justin A. Lemkul
Lum Ngwagia wrote: Hello everyone, I have been struggling to find a way to supply initial coordinates and initial velocities to a molecule like pentane. I want to add about 2500 molecules of pentane to a box, but all these molecules must have initial positions and velocities. I have

[gmx-users] Re: 3 covalent bonds protein- heme (malve...@iq.usp.br)

2009-09-17 Thread Gerrit Groenhof
ds, Yang Ye -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20090917/90a04153/attachment.html -- ___ gmx-users mailing list gmx-users@gromacs.org http:/

RE: [gmx-users] Core i7 vs Core2Quad

2009-09-17 Thread Berk Hess
That is nearly correct. For a single 4-core Intel Core I7 cpu, the first 4 cpu's (as well as the last 4) cover all 4 physical cores. Therefore the command line (under Linux) is: mpirun -np 4 taskset 0xf mdrun But you get 15% more performance using 8 processes (if your system is not too small): mp

[gmx-users] Re: 3 covalent bonds protein- heme

2009-09-17 Thread Thomas Schlesier
Yes, you must put the heme and the protein in the same topology file (or .itp file). The problem is you can only make bonds (angles, etc) between atoms which are in the same [ moleculetype ] section. Best is to write a simple script which merges the two topologies together. You must only be aware t

Re: [gmx-users] Periodic Boundary Conditions & Location of Atoms Near Box Edges

2009-09-17 Thread Tsjerk Wassenaar
Hi Darrell, No, you just have to make sure that the bond lengths are correct in the periodic system. The PBC are invariant under translation. Cheers, Tsjerk On 9/17/09, Darrell Koskinen wrote: > Dear GROMACS Gurus, > In order to correctly model an infinite graphene sheet using periodic > boun

[gmx-users] Re: Generating initial coordinates and velocities from scratch

2009-09-17 Thread Thomas Schlesier
Look in the manual for 'genbox', with this tool you can make a box with as many molecules you like. For the velocity generation look under *surprise* 'Velocity generation'. The manual is your friend, look in it. Greetings Thomas > > Hello everyone, > >I have been struggling to find a way

Re: [gmx-users] Large fluctuation of protein temperature with nose hoover thermostat

2009-09-17 Thread ABEL Stephane 175950
0171398 > T-Protein 310 32.1134 32.1117 -4.10352e-05 -1.14898 > T-Non-Protein 310 2.47549 2.47548 8.55869e-07 0.0239643 > -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/200909

[gmx-users] Inflategro

2009-09-17 Thread ram bio
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,

Re: [gmx-users] Inflategro

2009-09-17 Thread Justin A. Lemkul
ram bio wrote: 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 a

Re: [gmx-users] Inflategro

2009-09-17 Thread Pramod Akula
Dear Justin, Thanks for the suggestions. will be back aftersome time as i am redoing it. Please check me for the accuracy in steps in near future. Ram On Thu, Sep 17, 2009 at 8:20 PM, Justin A. Lemkul wrote: > > > ram bio wrote: > >> Dear Gromacs Users, >> >> While I was runing the Justin's

[gmx-users] GMX 4.0.5 on Altix 3700 BX2: Assembly Optimizations fixed?

2009-09-17 Thread Steve Cousins
I have installed Gromacs 4.0.5 on a 64 CPU Altix 3700 BX2 and when running mdrun it just seems to spin there. It uses 100% of one CPU but doesn't finish. I scanned through the list and found that I should try setting the NOASSEMBLYLOOPS environment variable. By doing this it runs now and the

[gmx-users] free energy problem

2009-09-17 Thread Elio Cino
Hello. I am trying to run free energy calculations on a protein - protein complex. I believe that I have made all of the necessary changes to my topology, and the nonbonded parameters are set to 0 for state B. I am using the GROMOS96 53a6 ff. My system runs fine with free energy turned off, but giv

Re: [gmx-users] GMX 4.0.5 on Altix 3700 BX2: Assembly Optimizations fixed?

2009-09-17 Thread Carsten Kutzner
Hi Steve, I made some tests on an Altix 4700 some time ago because I ran into the same problem. If you use the fortran loops (--enable-fortran, which is the default on sgi) you do not loose much performance. Here are my benchmark results with a 8 atom protein+bilayer+water simulation on a sin

Re: [gmx-users] about intermolecular interactions

2009-09-17 Thread Manik Mayur
2009/9/16 wuxiao > Dear GMXers, > > For long time, I have had a puzzle: while the top file generally describe > interactions in a molecule, intermolecular interactions are not explicitly > in the top file. How are these intermolecular interactions described in > GROMACS? Thanks a lot for any r

[gmx-users] (no subject)

2009-09-17 Thread rsf
Hi I have a silly question about the implementation of the Gromos forcefield in gromacs, particularly about the exclusions. I have the gromos manual and have seen that, for instance, for the residue MET there are only 1st and 2nd neighbors exclusions defined for it. However, when I build a protei

[gmx-users] generation of kernels

2009-09-17 Thread aherz
Hi, I'm having some problems compiling the latest development build from the git using fortran kernels. The nb_kernel_f77_single.c file includes lot's of headers which are incorrect (e.g. "nb_kernel410_f77_single.h") the proper file name has no underline after nb ("nbkernel410_f77_single.h"). I tr

Re: [gmx-users] generation of kernels

2009-09-17 Thread aherz
actually it's the other way around, it should be "nb_kernel410_f77_single.h" but the c file contains "nbkernel410_f77_single.h" Alex aherz schrieb: > Hi, > > I'm having some problems compiling the latest development build from the > git using fortran kernels. > The nb_kernel_f77_single.c file

Re: [gmx-users] GMX 4.0.5 on Altix 3700 BX2: Assembly Optimizations fixed?

2009-09-17 Thread Steve Cousins
On Thu, 17 Sep 2009, Carsten Kutzner wrote: Hi Steve, I made some tests on an Altix 4700 some time ago because I ran into the same problem. If you use the fortran loops (--enable-fortran, which is the default on sgi) you do not loose much performance. Here are my benchmark results with a 8000

Re: [gmx-users] GMX 4.0.5 on Altix 3700 BX2: Assembly Optimizations fixed?

2009-09-17 Thread David van der Spoel
Steve Cousins wrote: On Thu, 17 Sep 2009, Carsten Kutzner wrote: Hi Steve, I made some tests on an Altix 4700 some time ago because I ran into the same problem. If you use the fortran loops (--enable-fortran, which is the default on sgi) you do not loose much performance. Here are my benchma

[gmx-users] ISO-8859-1?Q? fixed=3F?=

2009-09-17 Thread Steve Cousins
On Thu, 17 Sep 2009, Discussion list for GROMACS users wrote: Since there is a 10% speedup by going back to version 3.3, is there any reason *not* to use 3.3 instead on the Altix? I'm sure there are other bug fixes and features since then but I don't know much about MD so I don't know how impor

Re: [gmx-users] Unit of RMSD of g_energy -f -f2

2009-09-17 Thread Mark Abraham
Ragnarok sdf wrote: Is the RMSD given by g_energy -f -f2 in Joule or KJoule? Units are described in section 2.2 of the manual. For g_energy, the units will obviously depend on the quantity involved. Mark ___ gmx-users mailing listgmx-users@grom

[gmx-users] butane-parameters

2009-09-17 Thread rversace
Hi Everybody: I am trying to perform a MD simulation of n-butane. But I cannot find the gromacs paramaters for it. In the 2005 paper from Lange about Flooding in GROMACS (J.Comp.Chem 21:1693.2006), the authors performed this simulation before using the ffgmx united atom force field. But I canno

Re: [gmx-users] butane-parameters

2009-09-17 Thread Justin A. Lemkul
rvers...@ccny.cuny.edu wrote: Hi Everybody: I am trying to perform a MD simulation of n-butane. But I cannot find the gromacs paramaters for it. In the 2005 paper from Lange about Flooding in GROMACS (J.Comp.Chem 21:1693.2006), the authors performed this simulation before using the ffgmx unite

[gmx-users] Force output from Distance Constraint on pair of Cations

2009-09-17 Thread Joshua D Monk
Hello everyone. I have seen a lot of post for the PULL function in Gromacs 4.0. ( I am using Gromacs 4.0.3) I have also been trying to use this function and I had a question about the Force output. The system I am working with is a pair of Ionic Liquids in spc216 solution. I want to fi

[gmx-users] SHAKE and LINCS

2009-09-17 Thread Ricardo O. S. Soares
Hello everyone, which one is used by default in case I do not provide any of them in the mdp file for molecular dynamics? Thanks! --- Ricardo O. S. Soares , MsC. Group of Biological Physics - Department of Physics & Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - Univer

[gmx-users] Re: Another problem with DNA

2009-09-17 Thread Gunnar Widtfeldt Reginsson
I tried to modify the spc.itp file, but wasn't successful. I decided not to try any more and changed to the amber_tip4p water model in the .top file. That solved the problem, no more error messages. Thanks for your help. On Wed, Sep 16, 2009 at 7:30 PM, Gunnar Widtfeldt Reginsson < regins...@gma

Re: [gmx-users] SHAKE and LINCS

2009-09-17 Thread Justin A. Lemkul
Ricardo O. S. Soares wrote: Hello everyone, which one is used by default in case I do not provide any of them in the mdp file for molecular dynamics? You'll have to define "any of them," because if you do not specify the "constraints" keyword in the .mdp file, then no constraints are use

[gmx-users] Re: gmx-users Digest, Vol 65, Issue 104

2009-09-17 Thread Ragnarok sdf
> > Ragnarok sdf wrote: > > Is the RMSD given by g_energy -f -f2 in Joule or KJoule? > > Units are described in section 2.2 of the manual. For g_energy, the > units will obviously depend on the quantity involved. > > Mark > > Well, that is the reason of my question. My FEP step when analysed with "

Re: [gmx-users] SHAKE and LINCS

2009-09-17 Thread Mark Abraham
Justin A. Lemkul wrote: Ricardo O. S. Soares wrote: Hello everyone, which one is used by default in case I do not provide any of them in the mdp file for molecular dynamics? You'll have to define "any of them," because if you do not specify the "constraints" keyword in the .mdp file, th

[gmx-users] analyzing gromacs trajectories on VMD

2009-09-17 Thread Amit Choubey
hi everyone, I want to analyze the gromacs trajectories using vmd, is there a quick way of doing so ? Is there a reference for this? Thank you Amit ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Pl

[gmx-users] Gromacs using MKL with Intel 11.1 compilers

2009-09-17 Thread Steve Cousins
I just thought I'd mention some troubles and fixes I had with trying to get Gromacs 4.0.5 to configure with --with-fft=mkl on a SGI Altix 3700 BX2 system. I did: export CC=icc export F77=ifort export CFLAGS="-O3 -ip -ftz" export FFLAGS="-O3 -ip -ftz" export LDFLAGS="-O3 -ip -ftz -L/opt/intel

Re: [gmx-users] analyzing gromacs trajectories on VMD

2009-09-17 Thread Justin A. Lemkul
Amit Choubey wrote: hi everyone, I want to analyze the gromacs trajectories using vmd, is there a quick way of doing so ? Is there a reference for this? Depends on what you want to analyze, but probably the VMD tutorials and manual will be the right place to start. -Justin Thank you

Re: [gmx-users] Gromacs using MKL with Intel 11.1 compilers

2009-09-17 Thread Mark Abraham
Steve Cousins wrote: I just thought I'd mention some troubles and fixes I had with trying to get Gromacs 4.0.5 to configure with --with-fft=mkl on a SGI Altix 3700 BX2 system. I did: export CC=icc export F77=ifort export CFLAGS="-O3 -ip -ftz" export FFLAGS="-O3 -ip -ftz" export LDFLAGS="-O3

[gmx-users] merging simulation boxes

2009-09-17 Thread Paymon Pirzadeh
Hello, Are there any links on how we can merge two simulation boxes to make a single configuration? What technicalities should be considered? Payman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] merging simulation boxes

2009-09-17 Thread Mark Abraham
Paymon Pirzadeh wrote: Hello, Are there any links on how we can merge two simulation boxes to make a single configuration? What technicalities should be considered? Define "merge". There's a whole pile of issues depending what you mean. Why can't you build initial coordinates up from scratch,

Re: [gmx-users] merging simulation boxes

2009-09-17 Thread Paymon Pirzadeh
I have a box of crystal (from another simulation) and a box of solvated protein. Now I want to put the protein close to my crystal. Payman On Fri, 2009-09-18 at 09:04 +1000, Mark Abraham wrote: > Paymon Pirzadeh wrote: > > Hello, > > Are there any links on how we can merge two simulation boxes

Re: [gmx-users] merging simulation boxes

2009-09-17 Thread Mark Abraham
Paymon Pirzadeh wrote: I have a box of crystal (from another simulation) and a box of solvated protein. Now I want to put the protein close to my crystal. Throw the water away, so you have two coordinate files, one of protein and one of crystal each in the same format. You can translate and ro

Re: [gmx-users] merging simulation boxes

2009-09-17 Thread Justin A. Lemkul
Paymon Pirzadeh wrote: I have a box of crystal (from another simulation) and a box of solvated protein. Now I want to put the protein close to my crystal. Use editconf to define a box for your new system, use -center on each component as appropriate, and cat the two .gro files together (rem

Re: SV: SV: SV: [gmx-users] g_order version 4.0.x

2009-09-17 Thread Justin A. Lemkul
Mauricio Carrillo Tripp wrote: Dear Justin, could you please tell me the right way of creating the index file to use with g_order v4.0.5? I found a discussion about it at http://www.mail-archive.com/gmx-users@gromacs.org/msg19885.html however, the following link has been down for a while: h

[gmx-users] question about chain identifier

2009-09-17 Thread Amit Choubey
hi everyone, I had a question about the purpose of chain identifier character in pdb. What does it mean for Gromacs, i mean what does gromacs do with it? I actually have a "bad" pdb file which has *different* chain identifiers for first few molecules of the same type and then there exists none for

Re: [gmx-users] analyzing gromacs trajectories on VMD

2009-09-17 Thread TJ Piggot
If you just want to a visual inspection of the trajectory then the easiest way is to type: vmd X.gro Y.xtc Where X is the name of your structure file and Y the name of your trajectory Tom --On Thursday, September 17, 2009 14:51:57 -0700 Amit Choubey wrote: hi everyone, I want to analyz

[gmx-users] Can Gromacs produce the data from NMR?

2009-09-17 Thread Chih-Ying Lin
HI Can Gromacs produce the data from NMR? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post

Re: [gmx-users] Gromacs using MKL with Intel 11.1 compilers

2009-09-17 Thread Vasilii Artyukhov
Hi, > Anybody have any real-world comparisons of using MKL vs. FFTW3? > http://www.quantumespresso.org/user_guide/node16.html says: Axel Kohlmeyer suggests the following (April 2008): "(I've) found that Intel is now turning on multithreading without any warning and that is for example why their

Re: [gmx-users] Can Gromacs produce the data from NMR?

2009-09-17 Thread Mark Abraham
Chih-Ying Lin wrote: HI Can Gromacs produce the data from NMR? No, if my guess at what "data" you mean is right. Why don't you ask a full question? :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/list

RE: [gmx-users] question about chain identifier

2009-09-17 Thread Berk Hess
Hi, The only program that really uses chain identifiers is pdb2gmx. It uses chain identifiers to recognize different protein (or DNA) molecules that appear sequentially in pdb files. All other programs will read chain identifiers and write them out again. Also Gromacs will add chain identifiers f