[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 t

[gmx-users] Re: Re:g_cluster output

ructures of the clusters are correct or not. Thanks 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

[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 adde

[gmx-users] Problem with version of gromacs

facing this problem , because I am trying to install it in a 64 bit computer? 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 mailin

[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 instal

[gmx-users] problem normal mode analysis

on 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

[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 a

[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

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 comman

[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 ./conf

[gmx-users] query regarding normal mode analysis

I try again to reduce the Fmax in energy 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/li

[gmx-users] query regarding normal mode analysis

I try again to reduce the Fmax in energy 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/li

[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] 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 no

[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] 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 t

[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 "la

[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 --- Begin Message ---  Dear Carsten, Thanks for your

[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

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

 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 it again? On Thu, 06 Nov 2008 Martin Höfling wrote : >You're probably not in a source directory. > >As you

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

[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] adding NH2 cap to C terminal

 Hi, I want to add -NH2 to the c terminal end of my peptide. If I modify the " C-terminal databse"-> "-c.tdb" , will it be possible to add -NH2 to the "CO" end of the last residue at the C terminal end. Thanks in advance, Sarbani ___ gmx-users

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

files 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

[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] 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: W

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

[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 thro

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: >>

[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 chatto

[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 . H

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 R

[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 pr

[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 a

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

[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 s

[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] 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 corresspond

[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] 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

han that. > >-Justin > >Quoting 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 > &g

[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 topol.top:696

[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 2>&1 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, line 141. I am not being able to make out what the error can be. please help in solving the

[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 tip4

Re: Re: [gmx-users] tip3p.gro

15 May 2008 10:28:13 - > "sarbani chattopadhyay" <[EMAIL PROTECTED]> wrote: >> 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 '

[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] 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 share/gro

[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 fo

[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 microstate

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 comp

[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] 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 du

[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 work

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 chattopadh

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 >>tpbc

[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 concatena

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

s different from a fit >against coordinates from the end or midway 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 > &g

[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 counterion

[gmx-users] extract protein and counter ions from trajectory

  Hi everybody, I want to know is there any way to extract the coordinates of both the protein and counterions from the trajectory while writing the "pdb" file ie. I don't want the water molecules but only the protein and the counter ions. I did not see that option wile t

[gmx-users] to add counter ions based on potential

  Hi everybody, I want to add counter ions based on potential and not randomly. I will be very grateful if anyone can guide me through the command "genion" for this. I tried with "-random no" but it didn't work. Thanks in advance Sarbani_

[gmx-users] g_nmeig_d error

ill 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

[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 show

[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] (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 'md

[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?

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 n

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

[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-use

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 grou

[gmx-users] queue up simulations

 hi, I want to know is there any way to 'queue up mdrun jobs' so that once one job is finished, the next starts automaticaly? Thanks in advance. Sarbani ___

[gmx-users] Fwd: trjconv help

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

[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 advance.

[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 advance.___

[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'= y