Re: [gmx-users] g_order in Gromacs 3.3.1

Arneh Babakhani wrote: Prof. Van Der Spoel, Regarding your suggestion here: Where exactly are lines 579 and 580 that one must modify? (I'm having this same error) In the gromacs source tree, file src/tools/gmx_order.c This file contains the body of code for which g_order.c is a stub. Mar

Re: [gmx-users] oplsaa dihedral with minimum at 222 degrees

Ben Harland wrote: I am preparing a topology for an opls-aa ATP molecule. It seems to me that one does not yet exist. I am having difficulties with the dihedral parameters: the OPLS-AA force field uses a RB-type function with a minimum at 180 degrees, but our QC data describes a function sym

Re: [gmx-users] Best FF for Morse Potential

Егоров Д.А. wrote: Dear Gromacs list members, Is it possible to choose best force field to extract bond constants to reevaluate them into Morse potential parameters? Harmonic bond potentials can be automatically converted to Morse. Check the file share/gromacs/top/edissoc.dat for dissociati

Re: [gmx-users] Position restrain

Alessandro Mattozzi wrote: While running a MD of PE with position restrain, i get this error message Fatal error: [ file "posre.itp", line 6 ]: Atom index (101) in position_restraints out of bounds (1-12) My atom index goes up to 6000, why do I have to be in the 1-12 range? your mo

Re: [gmx-users] Lipid Order Parameters - Calculating & Plotting

Hi Pedro, thank you for your prompt reply. I'm attempting to do what you suggested. 1). I create an index file, called sn2.ndx, which contains 14 groups, one group for each carbon type in the chain (labeled C2A, C2B, . . . C2N). 2) I then try to execute the following command: g_order -f Ful

Re: [gmx-users] g_order in Gromacs 3.3.1

Prof. Van Der Spoel, Regarding your suggestion here: Where exactly are lines 579 and 580 that one must modify? (I'm having this same error) Thanks, Arneh David van der Spoel wrote: Sukit Leekumjorn wrote: Dear GMX users, I have encounter some problem with g_order in Gromacs3.3.1. I no

RE: [gmx-users] channel in popc

> I try to use make_hole program to make a hole in popc > and input ion channel in it.whould you please help me? Try a search of this emailing list, which you do via the website. Details on how to do this have been metioned a few times. I have no idea how it is done and have never done it myself

[gmx-users] oplsaa dihedral with minimum at 222 degrees

I am preparing a topology for an opls-aa ATP molecule. It seems to me that one does not yet exist. I am having difficulties with the dihedral parameters: the OPLS-AA force field uses a RB-type function with a minimum at 180 degrees, but our QC data describes a function symmetric about 222 de

Re: [gmx-users] PDB2GMX PROBLEM: *** buffer overflow detected ***: pdb2gmx terminated

Anthony Cruz wrote: Hi: I want to run a simulation of a heme protein. I found that in the gromacs site the bug in the specbond.c and I download this file from bugzilla. I substitute this file in the source and try to build a new rpm to install. When I instal the new rpm and try to use pdb2gmx

Re: [gmx-users] Normal mode analysis - reference [34] in the Gromacs manual

Ran Friedman wrote: It seems like reference #34 in the GMX 3.3 manual should be: Levitt, M., Sander, C. and Stern PS. The normal modes of a protein: native bovine pancreatic trypsin inhibitor. Internatl. J. Quant.Chem., Quantum Biology Symposium 10, 181-199. 1983 And not as written. Ran. th

[gmx-users] POPC simulation

Hi All,thanks to Steffan , Jim and Kaushal for helping me out in the POPC simulation setup. i finally got everything to work. i guess the imp thing was to change the POPC to POP in .top file. thanks once again.Arindam Ganguly ___ gmx-users mailing list

Re: [gmx-users] Problem: parallel inefficient scaling with Mac Intel Core Duo

Yiannis wrote: Hello, Has anybody tried to use gromacs in parallel with the Intel Core Duo macintoshes? I installed gromacs and lam on some iMac with intel core duo 2x1.83GHz running the latest OSX with all updates. I have everything working OK but the scaling is very inefficient. Here are

Re: [gmx-users] total energy of system is positive,MD normal ?

linfu wrote: Dear all! My Simulation was done in decane and dmso. during analysis(g_energy), i find the energy of the whole system is positive not negative.however, fluctuation of temperature ,pressure and total energy is normal. Could anyone help me to figure out whether this MD is normal or

Re: [gmx-users] pair interaction in ligand topology file

Do you mean, "use pair interactions"? If you're referring to the [ pairs ] section of your topology, well, you will probably need to look at details on the force field to see what it expects, as the answer to this is force field dependent, and I don't typically use OPLS-AA. The [ pairs ] section i

Re: [gmx-users] TI, sampling, sc_power, and sc_alpha

My take is that it is preferable to partition your vdW and charge changes into two separate calculations, as the soft core settings that work well for the vdW portion make the charging portion a more "difficult" transformation than normal, and the settings that work well for charging make the vdW

Re: [gmx-users] Lipid Order Parameters - Calculating & Plotting

Check previous questions to the mailing list: http://www.gromacs.org/pipermail/gmx-users/2002-January/000527.html http://www.gromacs.org/pipermail/gmx-users/2004-February/009182.html --- Arneh Babakhani <[EMAIL PROTECTED]> wrote: > Hello GROMACS community, > > I was wondering if somebody cou

Re: [gmx-users] Lipid Order Parameters - Calculating & Plotting

Hello GROMACS community, I was wondering if somebody could walk me through the process of calculating lipid order parameters (for a DMPC membrane), using the g_order analysis tool? I've got a 5 ns trajectory and would like to make one of the classic order parameter plots: i.e. On the y-axis: t

RE: [gmx-users] TI, sampling, sc_power, and sc_alpha

From: [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] TI, sampling, sc_power, and sc_alpha Date: Fri, 26 May 2006 12:36:20 -0700 (PDT) Greetings once again fellow Gromacs-users, I have seen a substantial and disturbing change in c

Re: [gmx-users] Best FF for Morse Potential

Егоров Д.А. wrote: Dear Gromacs list members, Is it possible to choose best force field to extract bond constants to reevaluate them into Morse potential parameters? It depends what you want to use the potential for, and it is probably a bad idea. The bond constants are members of a paramet

Re: [gmx-users] Simulating crystalls

I am sorry.My system does not explode. It just kind of fuses. The atoms come close together and form a rounded mass. - karamyog.On 5/29/06, karamyog singh <[EMAIL PROTECTED]> wrote: However if the gen_velocity breaks up my system and at the end of my simulation, I do not get a bcc structure at lets

Re: [gmx-users] Simulating crystalls

You're on your own here unless you can provide more information. here is my .mdp file too. - karamyog. title    = Yo cpp  = /usr/bin/cpp include

[gmx-users] Position restrain

Title: Position restrain While running a MD of PE with position restrain, i get this error message Fatal error: [ file "posre.itp", line 6 ]: Atom index (101) in position_restraints out of bounds (1-12) My atom index goes up to 6000, why do I have to be in the 1-12 range? Regar

[gmx-users] Best FF for Morse Potential

Dear Gromacs list members,   Is it possible to choose best force field to extract bond constants to reevaluate them into Morse potential parameters?   D. Egorov, USMA, Yekaterinburg, Russia. ___ gmx-users mailing listgmx-users@gromacs.org http:/

Re: [gmx-users] Simulating crystalls

karamyog singh wrote: However if the gen_velocity breaks up my system and at the end of my simulation, I do not get a bcc structure at lets say 273 K, which I am not getting, then how can I consider my simulation to be correct? The structure should remain the same. I don't get the impression

Re: [gmx-users] Simulating crystalls

However if the gen_velocity breaks up my system and at the end of my simulation, I do not get a bcc structure at lets say 273 K, which I am not getting, then how can I consider my simulation to be correct? The structure should remain the same. Or could it be that since my structure is a nano layer

[gmx-users] Normal mode analysis - reference [34] in the Gromacs manual

It seems like reference #34 in the GMX 3.3 manual should be: Levitt, M., Sander, C. and Stern PS. The normal modes of a protein: native bovine pancreatic trypsin inhibitor. Internatl. J. Quant.Chem., Quantum Biology Symposium 10, 181-199. 1983 And not as written. Ran. -- ---

[gmx-users] binutils error msg x86_64-unknown-linux-gnu

  hi friends, I am installing GMX on a 2xdual core opteron processor system running on linux 10.0 I install lam by disabling the fortran as ./configure -without-fc make make install I configure fftw ./configure --enable-floats --enable-mpi make make install distclean ./configure --enable-mpi

Re: [gmx-users] total energy of system is positive,MD normal ?

linfu wrote: > Dear all! > > My Simulation was done in decane and dmso. during analysis(g_energy), i find > the energy of the whole system is positive > not negative.however, fluctuation of temperature ,pressure and total energy > is normal. Could anyone help me to figure out > whether this MD i

Re: [gmx-users] pair interaction in ligand topology file

4tejender wrote: Dear Gromacs users, I am tring to bulid ligand topology using OPLSAA forcefield. I want to know that should i user pair interactions in the ligand topology. If yes what is criteria for chosing atom pairs for pair interactions I've no idea what you mean by "user pair interac

Re: [gmx-users] Re: parallel run hangs (not crashed)

[EMAIL PROTECTED] wrote: On Mark Abraham's suggestion I verified that mpirun isn't a local wrapper. However, he also suggested "mpirun may not play nicely with a single-processor script that subsequently runs an MPI child process". I forwarded this to our lab tech who was unsure what this meant

[gmx-users] pair interaction in ligand topology file

Dear Gromacs users, I am tring to bulid ligand topology using OPLSAA forcefield. I want to know that should i user pair interactions in the ligand topology. If yes what is criteria for chosing atom pairs for pair interactions with thanks teje ___

[gmx-users] Lipid Order Parameters - Calculating & Plotting

Hello GROMACS community, I was wondering if somebody could walk me through the process of calculating lipid order parameters (for a DMPC membrane), using the g_order analysis tool? I've got a 5 ns trajectory and would like to make one of the classic order parameter plots: i.e. On the y-axis: the

Re: [gmx-users] install woe: Cannot find fftw3f library (Cygwin Bash)

Ralf B. Lukner wrote: During the ./configure of gromacs on my Cygwin Bash Shell, I get the following error: configure: error: Cannot find fftw3f library I have installed fftw3, but evidently not to the satisfaction of gromacs. I put the fftw3.h in usr/local/include, and that enabled me to m

[gmx-users] FW: Position restrain

Title: FW: Position restrain Hi gmx-users While running a MD of PE with position restrain, i get this error message Fatal error: [ file "posre.itp", line 6 ]: Atom index (101) in position_restraints out of bounds (1-12) My atom index goes up to 6000, why do I have to be in the

[gmx-users] PDB2GMX PROBLEM: *** buffer overflow detected ***: pdb2gmx terminated

Hi: I want to run a simulation of a heme protein. I found that in the gromacs site the bug in the specbond.c and I download this file from bugzilla. I substitute this file in the source and try to build a new rpm to install. When I instal the new rpm and try to use pdb2gmx the progam stop with t

[gmx-users] Re: parallel run hangs (not crashed)

Can somebody post the particulars for how they submit a parallel run on their system along with the brand/version of MPI they use? Thanks everyone for recent help with parallel run hanging/crashing. I have determined that it must be a problem with the way that I am submitting the parallel job (i.e

[gmx-users] channel in popc

Hi freinds I try to use make_hole program to make a hole in popc and input ion channel in it.whould you please help me? mahbubeh __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___

Re: [gmx-users] too long a simulation.

Hi Karamyog,You fail to mention what type of simulation (EM? MD?) and how long you're trying to simulation (ps? ns? mus?). 8 hrs doesn't sound very long to me if it's for a production run. I usually count months. But then again, your system is in fact small to my standards ;) Cheers,TsjerkOn 5/26/0

Re: [gmx-users] removing some solvent molecules

gil claudio wrote: I have a simulation box with a polymer in the middle and solvent molecules surrounding it. The box ended up being much bigger than needed--I'll need to reduce its size from 20.0 nm to 15 nm, removing solvent molecules in the process. Is there a way to do this? Generate fewe

Re: [gmx-users] PDB2GMX PROBLEM: *** buffer overflow detected ***: pdb2gmx terminated

Anthony Cruz wrote: Hi: I want to run a simulation of a heme protein. I found that in the gromacs site the bug in the specbond.c and I download this file from bugzilla. I substitute this file in the source and try to build a new rpm to install. When I instal the new rpm and try to use pdb2gmx

Re: [gmx-users] too long a simulation.

karamyog singh wrote: Dear gromaxers, I havea system of 6500 atoms. Gromacs shows that the simulation will take 8 hrs to complete the simulation. Is my system that large? The system is 15x15x15 units cells of Fe. so the the total box size is 4.305. I have tken cu-offs for LJ as 1.55. There is o

Re: [gmx-users] bad contacts and/or reduc

Hi Davood,Although there could be many causes, in this case I'd suspect that there is a water molecule trapped inside the protein. This can be the result of solvation using genbox. An isolated water molecule can start to "rattle". It will get close to one side of the microcavity and "kicked" to the

Re: [gmx-users] Simulating crystalls

karamyog singh wrote: Does this give any clue. It shows large PE, KE and temp. Could that be a reason? More information required? Your PE is ridiculously large. You have order 10^5 kJ/mol of PE for every atom, and obviously that is only coming from your LJ function. Check how you generated th

[gmx-users] PDB2GMX PROBLEM: *** buffer overflow detected ***: pdb2gmx terminated

Hi: I want to run a simulation of a heme protein. I found that in the gromacs site the bug in the specbond.c and I download this file from bugzilla. I substitute this file in the source and try to build a new rpm to install. When I instal the new rpm and try to use pdb2gmx the progam stop with t

Re: [gmx-users] install woe: Cannot find fftw3f library (Cygwin Bash)

Ralf B. Lukner wrote: During the ./configure of gromacs on my Cygwin Bash Shell, I get the following error: configure: error: Cannot find fftw3f library I have installed fftw3, but evidently not to the satisfaction of gromacs. I put the fftw3.h in usr/local/include, and that enabled me to m

Re: [gmx-users] Coordinates of the Centre of Mass.

On Mon, 29 May 2006 12:14:04 +0530 "Annie Albin" <[EMAIL PROTECTED]> wrote: Hi all, I would like to know if there is a way by which we can get to know the coordinates of the centre of mass for the molecule/system? Since new to this fieldany suggestions would be of great help.

[gmx-users] removing some solvent molecules

I have a simulation box with a polymer in the middle and solvent molecules surrounding it. The box ended up being much bigger than needed--I'll need to reduce its size from 20.0 nm to 15 nm, removing solvent molecules in the process. Is there a way to do this? Thanks. Gil Claudio _

[gmx-users] POPC simulation

I previously posted my modifications to get POPE to work with OPLSAA. You could make the analogous changes to your system. The message was: [gmx-users] lipid.itp LJ-1,4 values involving water Wed May 3 20:44:51 CEST 2006 ___ gmx-users mailing listgm

[gmx-users] channel in popc

hi freinds I try to use make_hole program to make a hole in popc and input ion channel into it.whould you please help me ? mahboobeh __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _

[gmx-users] install woe: Cannot find fftw3f library (Cygwin Bash)

During the ./configure of gromacs on my Cygwin Bash Shell, I get the following error: configure: error: Cannot find fftw3f library I have installed fftw3, but evidently not to the satisfaction of gromacs. I put the fftw3.h in usr/local/include, and that enabled me to make it past the fftw3.h

Re: [gmx-users] Simulating crystalls

Does this give any clue. It shows large PE, KE and temp. Could that be a reason? More information required? However, I have chenged my system a bit. My conf.gro file has just 2 atoms. one at the origin and the other at the body center. I use genconf to create a mesh of 4x4x4 unit cells at a distan

[gmx-users] too long a simulation.

Dear gromaxers, I havea system of 6500 atoms. Gromacs shows that the simulation will take 8 hrs to complete the simulation. Is my system that large? The system is 15x15x15 units cells of Fe. so the the total box size is 4.305. I have tken cu-offs for LJ as 1.55. There is only LJ interaction. rslist

[gmx-users] Lipid Order Parameters - Calculating & Plotting

Hello GROMACS community, I was wondering if somebody could walk me through the process of calculating lipid order parameters (for a DMPC membrane), using the g_order analysis tool? I've got a 5 ns trajectory and would like to make one of the classic order parameter plots: i.e. On the y-axis

[gmx-users] Problem: parallel inefficient scaling with Mac Intel Core Duo

Hello, Has anybody tried to use gromacs in parallel with the Intel Core Duo macintoshes? I installed gromacs and lam on some iMac with intel core duo 2x1.83GHz running the latest OSX with all updates. I have everything working OK but the scaling is very inefficient. Here are the results of t

[gmx-users] bad contacts and/or reduc

Dear gmx-users We want to study interaction of ligand to enzyme. We constructed the gro and top file from Prodrg and add it to the end of enzyme gro and change the number of atoms. Some of calculation carried out until mdrun of pr.mdp, but in this step we encontered to following error. what is the

[gmx-users] TI, sampling, sc_power, and sc_alpha

Greetings once again fellow Gromacs-users, I have seen a substantial and disturbing change in calculated free energy differences between systems run with Gromacs 3.3 and Gromacs 3.3.1. I am trying to determine if these differences are due to the new software, new parameters, insufficient sampli

[gmx-users] total energy of system is positive,MD normal ?

Dear all! My Simulation was done in decane and dmso. during analysis(g_energy), i find the energy of the whole system is positive not negative.however, fluctuation of temperature ,pressure and total energy is normal. Could anyone help me to figure out whether this MD is normal or not! Thank you

[gmx-users] Coordinates of the Centre of Mass.

Hi all,    I would like to know if there is a way by which we can get to know the coordinates of the centre of mass for the molecule/system?    Since new to this fieldany suggestions would be of great help. Thank you, Annie Albin. ___ gmx-use