[gmx-users] Re:Re: g_nmeig_d error:cannot allocate region

Hi, I had checked and found that gromacs has been compiled in 64 bit mode. However still I am getting this error with g_nmeig_d command which says g_nmeig_d(1892) malloc: *** mmap(size=18446744072353271808) failed (error code=12) *** error: can't allocate region I am running this on a 8

[gmx-users] g_nmeig_d error

will be of great help. Thanks in advance. Sarbani Chattopadhyay-- 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 (un)subscribe requests to the list. Use the www

[gmx-users] energy is coming nan

Hi , I am trying to simulate a protein in vacuum for 10 ns. However at around 8.8 ns the log file shows the following Step Time Lambda 4411700 8823.40.0 Energies (kJ/mol) Bond AngleProper Dih. Ryckaert-Bell.

[gmx-users] query regarding normal mode analysis

minimization step using switched cuolomb and van der waals interactions and then do NMA. Any suggestion will be of great help. Thanking You, Sarbani Chattopadhyay -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] query regarding normal mode analysis

minimization step using switched cuolomb and van der waals interactions and then do NMA. Any suggestion will be of great help. Thanking You, Sarbani Chattopadhyay -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] mdrun_d not running in parallel

Hi , I had installed gromacs4.0.7 in double preicision in 64 bit Mac 10.6.1 computer with 8 dual core processors. 1) I installed the fftw-3.0.1 in the following way ( in the directory) ./configure --enable float sudo make sudo make install make distclean

Re: RE: [gmx-users] g_nmeig_d error: can't allocate region

Hi Berk, Thanks for your reply. What is the correct way to compile gromacs in 64 bit mode? I installed fftw-3.0.1. using the following commands ./configure make sudo make install Then I downloaded the gromacs 4.0.7 source code and installed it using the following

[gmx-users] g_nmeig_d error: can't allocate region

Hi, I am trying to do normal mode analysis on a protein having 6398 atoms in vaccum. I tried to energy minimize the structure using steepest descent, followed by l-bfgs minimization. the .mdp file I used is define = -DFLEXIBLE constraints = none integrator

[gmx-users] energy minimization problem

Hi , I have a protein with 2 chains. I need to do normal mode analysis on it. As there are no covalent bonds between the two chains, I did not use the merge option in the pdb2gmx command. I am trying to energy minimize the structure , in vaccum.( in double precision) , but am not able

[gmx-users] problem normal mode analysis

help. Thanks in advance. Sarbani Chattopadhyay-- 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 (un)subscribe requests to the list. Use the www

[gmx-users] gromacs 4.0.7 compilation problem

Hi , I want to install gromacs 4.0.7 in double precision in a 64 bit Mac computer with 8 nodes. I got the lam7.1.4 source code files and installed them using the following commands ./configure --without-fc ( it was giving an error for the fortran compiler) make make

[gmx-users] Problem with version of gromacs

? is there anything else wrong? Is there any way to run this gromacs version on the 64 bit computer or should I try to install a newer version of gromacs? Thanks in advance Sarbani Chattopadhyay -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] grompp warning

Hi, I have a 13 residue peptide which I have kept in a box using the following command editconf -f conf.gro -bt cubic -o box.gro -d 0.75 the flag -d 0.75 is given as per the ' minimum image convention'. When I solvate the box, 6772 water molecules get

[gmx-users] Re: Re:g_cluster output

in advance, Sarbani. On Wed, 22 Apr 2009 15:32:07 +0530 wrote sarbani chattopadhyay wrote: Hi, I have a query regarding g_cluster output. I gave the command g_cluster -f ../const_temp_20ns_0.pdb -s ../../md_0.tpr -sz -tr -cl -wcl 25 -cutoff 0.2 It is written in the clusters.log file

[gmx-users] g_cluster output

Hi, I have a query regarding g_cluster output. I gave the command g_cluster -f ../const_temp_20ns_0.pdb -s ../../md_0.tpr -sz -tr -cl -wcl 25 -cutoff 0.2 It is written in the clusters.log file that the middle structures of each cluster is written in the clusters.pdb file. How is this

[gmx-users] questions regarding Replica Exchange

 Hi, I have few queries regarding Replica Exchange MD. 1) I have 17 replicas , and the files are named as md_0.trr,..,.md_16.trr.Replica exchange is attempted every 100ps. Thus starting from 0, upto 100ps, the coordinates, velocities etc. that are written in md_0.trr files

[gmx-users] k- means clustering

  Hi everyone, I want to know whether anyone has done k-means clustering using gromacs 3.3.1. I saw that one program has been contributed to do k-means clustering using g_cluster. Has anyone tried to use this program to do such clustering. I would also like to know the

[gmx-users] k means cluster

  Hi, Actually I was referring to the following post where the attempt to incorporate the method of k means clustering in gromacs has been discussed. http://www.mail-archive.com/gmx-users@gromacs.org/msg05089.html Has anyone tried to use this ? Thanks in advance Sarbani

[gmx-users] restarting a replica exchange simulations

 Hi, I had previously ran a replica exchange molecular dynamics simulation for 10ns. There were 17 .tpr input files for 17 replicas at 17 different temperatures. However, the run had stopped and now I need to restart it. I had generated 17 .tpr files for the rest of the

[gmx-users] REMD problem in concept

 Hi everybody, I am having a doubt whether I have understood the concepts of Replica exchange molecular dynamics correctly or not. When a pair of replicas are exchanged, the one at higher temperature thet has higher velocities, (which are rescaled

Re: Re: [gmx-users] REMD problem in concept

 Hi, Thank you for the reply. But in that case what helps the replica at higher temperature cross the energy barrier? At higher temperature the velocities will be higher. Thanks in advance, Sarbani On Tue, 02 Dec 2008 Mark Abraham wrote : sarbani chattopadhyay wrote: Hi everybody

[gmx-users] how many pairs are exchanged in replica exchange

  Hi, I am new to Replica exchange molecular dynamics. I obtained the optimal temperature distribution based on the lowest and highest tempearture and exchange probability from the REMD caclulator , available through the gromacs homepage. There were 17 temperaure values as output. I

[gmx-users] Replica exchange temp. distribution

  Hi everyone, I will like to do Replica exchange simulation on a peptide. We have a single machine with 4 cpus and the gromacs3.3.2 is installed. Thus I will be able to select only 4 temperature values. I came across the T-REMD caculator for temperature distributions .

Re: Re: [gmx-users] Replica exchange temp. distribution

possible method by which I can choose 4 optimal temperature values, maintaining a decent exchange-probability value? Thanks in advance, Sarbani On Wed, 19 Nov 2008 Mark Abraham wrote : sarbani chattopadhyay wrote: Hi everyone, I will like to do Replica exchange

Re: Re: [gmx-users] can't find fftw3f library

 Thank you Mark, I am sorry I didn't go through the Archive thoroughly before posting my query. I found that this problem had been addressed and solved in the past. Sarbani On Thu, 13 Nov 2008 Mark Abraham wrote : sarbani chattopadhyay wrote: Hi everybody

[gmx-users] lamboot command problem

  Hi everybody, I am facing problem while running parallel runs. Ours is a single Mac Os X machine with 2 dual core processors. Thus the hostfile taht I made was mac-pros-computer.local cpu=2 mac-pros-computer.local cpu=2 When I use the command lamboot I get the message

Re: Re: [gmx-users] lamboot command problem

 Thank you Mark, You are absolutely right. I made a mistake while giving the command. It is running fine after giving the command mpirun -np 4 mdrun_mpi THANK YOU VERY MUCH!!! Sarbani On Thu, 13 Nov 2008 Mark Abraham wrote : sarbani chattopadhyay wrote: Hi

[gmx-users] problem installing FFTW

  Hi everybody, I am trying to install FFTW and gromacs 3.3.2 into my Mac 10.4.1. I got the source code fftw-3.0.1.tar.gz. from GROMACS homepage . However, when I tried to configure FFTW, I found the message dummy main to link with Fortran 77 libraries... unknown configure:

[gmx-users] problem with FFTW installation

 Hi everybody, I am trying to install FFTW and gromacs 3.3.2 into my Mac 10.4.1. I got the source code fftw-3.0.1.tar.gz. from GROMACS homepage . However, when I tried to configure FFTW, I found the message dummy main to link with Fortran 77 libraries... unknown configure:

Re: Re: [gmx-users] problem with FFTW installation

 Thank you Mark. I will continue with the installation. Sarbani On Thu, 13 Nov 2008 Mark Abraham wrote : sarbani chattopadhyay wrote: Hi everybody, I am trying to install FFTW and gromacs 3.3.2 into my Mac 10.4.1. I got the source code fftw-3.0.1.tar.gz. from GROMACS

[gmx-users] can't find fftw3f library

  Hi everybody, I am trying to install gromacs3.3.2 into my Mac Os X 10.4.1 using the source code. I have installed FFTW and the library files of fftw are in /usr/local/lib. However when I try to configure gromacs, it's gives an error : Cannot find fftw3f library. Going

Re: Re: [gmx-users] adding NH2 cap to C terminal

do I need to modify ? Till now I have only modified the terminal database ,( though I may have made some mistake ), but the added N 's coordinates are given by pdb2gmx as nan nan nan Thanks in advance Sarbani On Mon, 10 Nov 2008 Mark Abraham wrote : sarbani chattopadhyay wrote: Hi

[gmx-users] files to modify to add NH2 cap at C terminal end

 Hi everyone, I had asked this question before but I will try to explain myself more clearly. I wan t to add -NH2 cap at the Cterminal end of my protein. I had included charmm force field into my gromacs 3.3.1. I had added the following into my ffcharmm-c.tdb file [NH2]

[gmx-users] can't find distclean

  Hi, I am facing a peculiar problem and may sound stupid, but I need help. We have a 10.4.1. Mac Os X machine with 2 dual core processors. I had downloaded gromacs 3.3.2 and installed it in this computer using installer. It added the gromacs directory into /usr/loca/ directory. I want

Re: Re: Re: [gmx-users] can't find distclean

2008 Martin Höfling wrote : Am Donnerstag, den 06.11.2008, 10:23 + schrieb sarbani chattopadhyay: Does this mean thai I can't recompile gromacs because I had used a binary package for installing gromacs. Isn't there any way in which I can compile gromacs, without having to install

[gmx-users] way to cap C-terminal as CONH2

 Hi everyone, I want to know is there any way to add Amide cap at the C terminal end of the protein using gromacs. Using pdb2gmx -ter doesnot give CONH2 as one of the options. Any suggestion is welcome. Thanks in advance Sarbani

[gmx-users] Fwd: still problem with lamboot

  Note: Forwarded message attached -- Original Message -- From: sarbani chattopadhyay [EMAIL PROTECTED] To: gmx_usrs [EMAIL PROTECTED] Subject: still problem with lamboot ---BeginMessage---  Dear Carsten, Thanks for your reply. As per your suggestion I tried

[gmx-users] problem with lamboot

 Hi everybody, I have question regarding parallel run. I am new to this and may sound very stupid so please bear with me. Our's is a 10.4.1 Mac Os X with 2 X 2.66 GHz Dual -Core Intel Xeon processor. Gromacs 3.3.1 was loaded in it. Then I had downloaded the

[gmx-users] range of gen_seed

  Hi everyone, I want to start from the same starting structure with different velocities. In the .mdp file. I used 3 different values for gen_seed for three different runs : 1. one is the default, the other two are 1 and 571. I want to know that does this ensure that the

[gmx-users] problem with genion

  Hi everyone, I am facing a peculiar problem with genion. I have a system with overall charge 0f +3. I want genion to add enough ions to make the cocncentration 10 micromoles/litre. When I give the command genion -s em.tpr -o ions.gro -conc 0.1 -pname NA+ -nname CL- -p

[gmx-users] question regarding genion

 Hi everybody, I want to place my counterions close to the charged amino acids. I am aware of the fact that even if the counterions are randomly added yet they will eventually settle during equlibration. But still I will like to start with a structure that has

[gmx-users] which tpr file to use

 Hi everyone, I am facing a peculiar problem. I had given an exteneded continuation run using the tpbconv command. The extended run had crashed due to power failure. I again gave an exact continuation run using the tpbconv command. After the run was over, I concatenated

Re: Re: [gmx-users] which tpr file to use

a run. Options like -pbc nojump add further restrictions to the reference file you use, but for that do browse the archives, as I don't feel like elaborating on that again. Cheers, Tsjerk On Thu, Sep 11, 2008 at 8:12 AM, sarbani chattopadhyay [EMAIL PROTECTED] wrote: Hi everyone

[gmx-users] problem with continuation of md

 Hi all, I had used the tpbconv command to give continuation run on a 2ns simulation. I had provided the previois trajectory file, energy file for this. However the continuation run had crashed due to power failure and I again had to give a rerun on it. Everything seems to be

Re: Re: [gmx-users] problem with continuation of md

 The post 2ns run had crashed. The commands were tpbconv -f 2ns.trr -e 2ns.edr -s 2ns.tpr -extend 1 When it crashed ,the command given was tpbconv -f ext10ns.trr -s ext10ns.tpr -e ext10ns.edr -o leftrun.tpr On Wed, 10 Sep 2008 Justin A.Lemkul wrote : sarbani chattopadhyay wrote: Hi

Re: Re: [gmx-users] problem with continuation of md

On Wed, 10 Sep 2008 Justin A.Lemkul wrote : sarbani chattopadhyay wrote: The post 2ns run had crashed. The commands were tpbconv -f 2ns.trr -e 2ns.edr -s 2ns.tpr -extend 1 When it crashed ,the command given was tpbconv -f ext10ns.trr -s ext10ns.tpr -e ext10ns.edr -o leftrun.tpr So

[gmx-users] LINCS error

 Hi, I am trying to simulate a peptide whose structure is yet to be validated experimentally. It has 3 protonated lysine residues. I have used oplsaa force filed with spc water model and had added 3 CL ions into the box. Everything works fine till energy minimisation but after that

[gmx-users] when gen_vel should be no

  hi, I want to know that in what situation does the initial velocity to the starting structure is to be kept at zero. thanks in advance sarbani___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] charmm and oplsaa simulation results don't match

  Hi everybody, I had run a long 100ns simulation on a tripeptide using opls/aa force field and spc water model. I got a few microstates. Then I tried to run simulation on the same system using charmm force field and tip3p water model. However I couldn't find the

Re: FW: [gmx-users] charmm and oplsaa simulation results don't match

hi,   Thanks for the suggestions. Actually the microstates are revisited in the 100ns span and one of them is occupied for longer time span than the others. I had broken the 100ns trajectory(oplsaa) in 3 parts and took starting structures from each of them and run simulations and obtained

[gmx-users] mistake!!

 Hi everybody, My question is regarding the consequence of a mistake of mine. I wanted to run gromacs with charmm force field and tip3p water model. I had posted a query as to how can I get the tip3p.gro file. I was suggested to equlibrate the spc216.gro file for 1ns.

[gmx-users] new version of C terminus database for charmm

  Hi, I am trying to run gromacs with charmm forcefield. # I had run the perl program convert_charmm_to_gromacs.pl and put the output files ffcharmmbon.itp and ffcharmmnb.itp into the gromacs share/gromacs/top directory. # I had put all the files from the tar file into the

[gmx-users] problem with charmm

 hi, I have followed the process as told by Yuguan Mu.But while using the comman pdb2gmax I get the following error Source code file: ter_db.c, line: 85 Fatal error: Reading Termini Database: expected 3 items of atom data in stead of 1 on line N NH314.0027-0.3000 I

[gmx-users] tip3p.gro

  Hi, I am trying to run gromacs using charmm using the tip3p water model. I need the tip3p.gro file for this. Is there any way to get it? I have a '.itp' file specificaly for tip3p with charmm but not for tip4p, though tip4p.gro is available . is there any way in which I can use the

[gmx-users] fix_top_for_charmm.pl problem

  Hi, I wanted to know the correct way to use the script fix_top_for_charmm.pl. i did the following : fix_top_for_charmm.pl grompp -f em.mdp -c b4em.gro -o em.tpr grompp grompp -f em.mdp -c b4em.gro -o em.tpr -maxwarn 999 21 1/dev/null Success! .top file did not need fixing for CHARMM

[gmx-users] error with fix_top_for_charmm.pl

  hi, i get the following error on running the command fix_top_for_charmm.pl -f em.mdp -c b4em.gro -p topol.top Use of uninitialized value in multiplication (*) at ./fix_top_for_charmm.pl line 177, GEN1 line 141. I am not being able to make out what the error can be. please help in

[gmx-users] grompp error with charmm

 hi, I am trying to run gromacs using charmm but I am facing the following error while running the grompp command checking input for internal consistency... calling /usr/local/bin/cpp... topol.top:11:24: /usr/local/gromacs/share/gromacs/top/ffcharmm.itp: Permission denied

[gmx-users] error running gromacs usinh charmm force field

 hi, I am trying to run gromacs using charmm force field. I run the perl program convert_charmm_to_gromacs.pl on the charmm force field input file. the following 2 files were generated ffcharmmbon.itp

Re: Re: [gmx-users] error running gromacs usinh charmm force field

sarbani chattopadhyay [EMAIL PROTECTED]:  hi, I am trying to run gromacs using charmm force field. I run the perl program convert_charmm_to_gromacs.pl on the charmm force field input file. the following 2 files were generated

[gmx-users] charmm force field

  hi, This is not specificaly A GROMACS related question. I want to do MD simulations using CHARMM force field using GROMACS. I am aware of the perl programs written by M. ABRAHAM and look forward to using it. I want to know which is the most convenient way in which I can get the CHARMM

[gmx-users] how to get charmm force field input file for MD

  hi, This is not specificaly A GROMACS related question. I want to do MD simulations using CHARMM force field using GROMACS. I am aware of the perl programs written by M. ABRAHAM and look forward to using it. I want to know which is the most convenient way in which I can get the CHARMM

[gmx-users] problem with extended run using grompp

  Hi, I used 'grompp' to get the '.tpr' file for extending my run. I had provided the trajectory file , energy file for the previous run and gave the value of the last step of the previous run for the 'init_step ' and the last time step for the ' t_init' and turned 'unconstrained start'=

[gmx-users] (no subject)

 hi, I want to extend my run, for which I will have to use 'tpbconv' command.But this time I want to change the frequencies in which the energies,velocities and 'xyz' coordinates will be written to the trajectory file. Is there any way to do it? Thanks in

[gmx-users] potential energy of only the protein

  hi, I want to get the potential energy of only the protein ie. without that of the water.'g_energy' calculates the energy from the energy file. The groups written for the energygroups are 'protein sol'. Is there any way to get the energy only of the protein? Thanks in

[gmx-users] Fwd: trjconv help

  Note: Forwarded message attached -- Original Message -- From: sarbani chattopadhyay [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: trjconv help ---BeginMessage---  hi, I had run MD simulations where the output control parameters were nstxout=250 nstvout= 1000

Re: Re: [gmx-users] make_ndx

 Thanks Mark, I could do it following your suggestion. Sarbani On Wed, 24 Oct 2007 Mark Abraham wrote : sarbani chattopadhyay wrote: hi, I want to select two groups in the index file

Re: Re: [gmx-users] Position restricted md

wrote : sarbani chattopadhyay wrote: Hi, I am new to the field of MD.I want to know what is the effectivity of position restricted MD ie. where is the advantage of doing Position restricted MD.I have a small peptide of 3 reidues.Is it necessary to do a Position restricted MD. What

Re: Re: [gmx-users] Position restricted md

 I understand.Thank you for the comparative analysis. sarbani On Tue, 23 Oct 2007 Mark Abraham wrote : sarbani chattopadhyay wrote: yes , I had gone through the manual, but is that all? I mean to say

[gmx-users] alpha Carbon-Aromatic ring hydrogen bond

 Hi, I want to analyze the Hydrogen bond between alpha Hydrogen and aromatic ring over the simulation time.g_hbond can't recognise this bond.is there any command by which i can do that?

[gmx-users] make_ndx

 hi, I want to select two groups in the index file, one group consisting of only the aromatic ring of phenylalanine and the other group consisting of only the alpha carbon. I want to know the way to use the make_ndx command for this. ___

[gmx-users] Position restricted md

  Hi, I am new to the field of MD.I want to know what is the effectivity of position restricted MD ie. where is the advantage of doing Position restricted MD.I have a small peptide of 3 reidues.Is it necessary to do a Position restricted MD. What difference will it make?

[gmx-users] (no subject)

 hi, I am using gromacs to run MD simulations using Intel dual core machine OSX (version 10.4.10) .I downloaded the 'already compiled gromacs package'. Is there any way to find whether the simulation process makes optimum usage of the 2 processors. Is there any command to direct the

[gmx-users] restart md from the point it had stopped

  hi, I have been running a molecular dynamics simulation for 2 nanoseconds.But it stopped in the middle because of an internal problem.Is there any way to restart the simulation from the point it has stopped?

[gmx-users] water molecules suffer from very long bond lengths

  hi , i am trying to use GROMACS to perform MOLECULAR DYNAMICS simulation on a small peptide. i gave the dimensions -d 0.75 in the 'editconf' command and then solvated the box and energy minimized it using 'l-bfgs' minimization process. i ran a simulation for 10 ps, but the trajectory