Re: [gmx-users] Parallel mdrun not working on gentoo linux

test programs are running fine. further, $mdrun_mpi just results in a blinking cursor at newline (earlier it displayed an array of info strings) Mark -Manik - Original Message - From: Manik Mayur manik.ma...@gmail.com Date: Saturday, August 14, 2010 15:14 Subject: [gmx-users

[gmx-users] Parallel mdrun not working on gentoo linux

is the problem? Thanks, Manik Mayur -- 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 interface or send it to gmx

[gmx-users] Problem using trjconv and g_potential

- g_potential -f Soln.trr -s Sim_ions.tpr -n Soln.ndx -o potential.xvg -oc charge.xvg -d Z Selected 4: 'Ions' trn version: GMX_trn_file (single precision) Reading frame 0 time 1000.000 Dividing the box in 10 slices Segmentation fault Thanks, Manik Mayur Graduate student Microfluidics Lab Dept

Re: [gmx-users] Hydrated radius of ions

a nail. *From:* gmx-users-boun...@gromacs.org [mailto: gmx-users-boun...@gromacs.org] *On Behalf Of *Manik Mayur *Sent:* Friday, 20 November 2009 2:10 AM *To:* Discussion list for GROMACS users *Subject:* [gmx-users] Hydrated radius of ions Hi, Is there any gromacs utility to calculate

[gmx-users] Hydrated radius of ions

Hi, Is there any gromacs utility to calculate the hydrated radius of ions? Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] pdb2gmx : treat CL as C

2009/11/17 Nilesh Dhumal ndhu...@andrew.cmu.edu this is the command, pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter Here I have attached the dioxin.pdb file. Check your dioxing.pdb.. there might be formatting issues. It might happen the due to bad format of the pdb file, your 'L' is

Re: [gmx-users] water molecule cannot be settled

2009/9/29 Justin A. Lemkul jalem...@vt.edu Carla Jamous wrote: Thank you for your reply, but none of the water molecules with error messages is trapped inside my protein, nor is it in contact with the protein or the ions in my system. Also if the water molecules are positioned properly,

Re: [gmx-users] about intermolecular interactions

before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA

Re: [gmx-users] bypassing pdb2gmx

use editconf -f file.pdb -o file.gro Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA 2009/9/10 Amit Choubey kgp.a...@gmail.com hi everyone, I have a pdb file of my system and i want it to be fed into the GROMACS software. I have a new force field

Re: [gmx-users] potential energy NaN and strange dependence on cut-offs

the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing listgmx

[gmx-users] Thermostats in a NEMD

with? Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Re: [gmx-users] Re: R: R: R: CNT

)). With regards, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA On Thu, Jul 30, 2009 at 5:56 PM, Vitaly V. Chaban vvcha...@gmail.comwrote: If you unzipped/untarred the archive properly it should be some system already prepared to run. So you can just

[gmx-users] Regarding binning technique

problem, how do you resolve it? Thanks and regards, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] 4.0.5 Installation error

to note is that I have successfully compiled and installed mpi version of mdrun on the same machine, for GROMACS-4.0.4. What am I missing here? Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users

[gmx-users] Re: 4.0.5 Installation error

On Mon, Jun 29, 2009 at 12:54 PM, Manik Mayur manik.ma...@gmail.com wrote: Hi, I am trying to install GROMACS-4.0.5, but while making mpirun with the option --enable-mpi it gives the following sets of errors: read making mdrun ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined

Re: [gmx-users] 4.0.5 Installation error

On Mon, Jun 29, 2009 at 1:51 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Manik Mayur wrote: Hi, I am trying to install GROMACS-4.0.5, but while making mpirun with the option --enable-mpi it gives the following sets of errors: ../gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.so: undefined

Re: [gmx-users] problem in ngmx

? Read http://www.gromacs.org/mailing_lists/users.php Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] Re: Issues regarding exclusions and Charge group distribution

: (nil) [md-comp1:32377] [ 0] [0xb7fd8440] [md-comp1:32374] [ 0] [0xb7ef0440] [md-comp1:32374] *** End of error message *** [md-comp1:32377] *** End of error message *** I would be extremely thankful, if somebody points me to the source of the error and the workaround. Thanks, Manik Mayur Graduate

Re: [gmx-users] Re: Issues regarding exclusions and Charge group distribution

On Fri, Jun 12, 2009 at 8:46 AM, Mark Abraham mark.abra...@anu.edu.auwrote: Manik Mayur wrote: Hi, The last mail supposedly bounced from the server due to attachments. So please excuse in case you find this as a repetition. I am trying to simulate a system where I want to exclude all nb

Re: [gmx-users] conversion to tip5p

the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing list

[gmx-users] Pressure and NVT Simulations

time of equilibration? Can anyone point me to fundamental theory pertaining to this behavior as I couldn't find any upon googling. Please do not suggest doing NPT as for some reason I want to avoid it for now. Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur

Re: [gmx-users] Pressure and NVT Simulations

On Fri, Jun 5, 2009 at 11:58 PM, Jussi Lehtola jussi.leht...@helsinki.fiwrote: On Fri, 2009-06-05 at 23:28 +0530, Manik Mayur wrote: Hi, I am trying to equilibrate a box of SPC/E water using NVT simulations. After 2 ns of equilibration my pressure is still 0 bars. Is it an expected

Re: [gmx-users] DSSP problem

to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing

[gmx-users] Some questions regarding generating topologies

) I am using GROMOS96 43a1, so am I allowed to change combination rule to '2' ( '1' is the default). How significantly will it affect the simulations? Any relevant idea/suggestion/reference is appreciated. Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT

Re: [gmx-users] Some questions regarding generating topologies

On Wed, Jun 3, 2009 at 9:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: Manik Mayur wrote: Hi, Even though after going through the manual, I still have some basic confusions regarding generating topologies. 1) I have generated an itp file after adding some Cl- ions using genion

Re: [gmx-users] installation

://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT

[gmx-users] Problem with pdb2gmx when used with OPLS and TIP4P

is the OW-HW3 bond is getting stretched? Also, what should be the correct procedure for the conversion? Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Problem with pdb2gmx when used with OPLS and TIP4P

On Thu, May 14, 2009 at 1:32 AM, Justin A. Lemkul jalem...@vt.edu wrote: Manik Mayur wrote: Hi Users, I constructed a .pdb file for TIP4P water model which I tried to convert to .gro using pdb2gmx using: $ pdb2gmx -f Sim1.pdb -o Sim1.gro -water tip4p There is no need to use pdb2gmx

Re: [gmx-users] Problem with pdb2gmx when used with OPLS and TIP4P

On Thu, May 14, 2009 at 1:56 AM, Justin A. Lemkul jalem...@vt.edu wrote: Manik Mayur wrote: On Thu, May 14, 2009 at 1:32 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Manik Mayur wrote: Hi Users, I constructed a .pdb file for TIP4P water model

[gmx-users] Couette flow

giving constant velocity to a group of atoms, as we can do in LAMMPS, in future versions. It will really be a life saver if GROMACS can be used for such problems. Also can we build GROMACS as a library to be called from customized codes? Thanks, -- Manik Mayur Graduate student Microfluidics Lab Dept

Re: [gmx-users] Couette flow

On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: Manik Mayur wrote: Hi, With reference to http://www.mail-archive.com/gmx-users@gromacs.org/msg13374.html I would like to know if anybody has successfully simulated couette flow using GROMACS. If yes

Re: [gmx-users] Couette flow

On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: Manik Mayur wrote: On Fri, Apr 3, 2009 at 8:25 PM, David van der Spoel sp...@xray.bmc.uu.semailto: sp...@xray.bmc.uu.se wrote: Manik Mayur wrote: Hi, With reference to http

Re: [gmx-users] Couette flow

On Fri, Apr 3, 2009 at 10:47 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: Manik Mayur wrote: On Fri, Apr 3, 2009 at 9:48 PM, David van der Spoel sp...@xray.bmc.uu.semailto: sp...@xray.bmc.uu.se wrote: Manik Mayur wrote: On Fri, Apr 3, 2009 at 8:25 PM, David van der

Re: [gmx-users] Couette flow

On Fri, Apr 3, 2009 at 11:11 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: Manik Mayur wrote: On Fri, Apr 3, 2009 at 10:47 PM, David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote: Manik Mayur wrote: On Fri, Apr 3, 2009 at 9:48 PM, David van der

Re: [gmx-users] Timestep and force field

...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

Re: [gmx-users] Compiler and OS issue in gromacs

/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 interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Manik

[gmx-users] mdrun hangs with the pull option

= 1 k= 0 kB = 0 The other useful data might be: OS- Ubuntu 8.04 Gromacs- 4.0.2 Thanks, Manik Mayur -- Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur md.log Description: Binary data eql.mdp Description: Binary

Re: [gmx-users] mdrun hangs with the pull option

8.04 Gromacs- 4.0.2 Thanks, Manik Mayur -- Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur -- Express yourself instantly with MSN Messenger! MSN Messengerhttp://clk.atdmt.com/AVE/go/onm00200471ave/direct/01

Re: [gmx-users] mdrun hangs with the pull option

On Tue, Mar 17, 2009 at 9:31 PM, Manik Mayur manik.ma...@gmail.com wrote: 2009/3/17 Berk Hess g...@hotmail.com Hi, You pull rate is ridiculously high (1 nm/ps). Also I am simulating in reduced dimentions. I think it is fine then. Is there any upper limit on the pull rate? btw

[gmx-users] Problem configuring openMPI

Hi, I have till now successfully used openMPI and gromacs together. Recently I got a cluster where I tried to install openMPI and gromacs locally as I donot have root priviledges on it. But it turns out that it already has MPI environment on it (LAM) which I donot want to use (as the version is

Re: [gmx-users] Problem configuring openMPI

often, though, you might need to use different Lam options. Nicolas Manik Mayur a écrit : Hi, I have till now successfully used openMPI and gromacs together. Recently I got a cluster where I tried to install openMPI and gromacs locally as I donot have root priviledges on it. But it turns out

Re: [gmx-users] Problem configuring openMPI

On Tue, Mar 3, 2009 at 11:47 PM, Nicolas nsa...@ucalgary.ca wrote: Manik Mayur a écrit : Hi, If I have 2 mpi environments, namely LAM and openMPI, and I want gromacs to use openMPI of the two, what extra option should I pass during the ./configure step? In my case openMPI is installed

Re: [gmx-users] Problem configuring openMPI

On Wed, Mar 4, 2009 at 12:28 AM, Nicolas nsa...@ucalgary.ca wrote: Manik Mayur a écrit : On Tue, Mar 3, 2009 at 11:47 PM, Nicolas nsa...@ucalgary.ca mailto: nsa...@ucalgary.ca wrote: Manik Mayur a écrit : Hi, If I have 2 mpi environments, namely LAM and openMPI, and I

Re: [gmx-users] Problem configuring openMPI

to `lam_rtrstore' collect2: ld returned 1 exit status make[1]: *** [mdrun] Error 1 what is the problem now? On Wed, Mar 4, 2009 at 12:43 AM, Manik Mayur manik.ma...@gmail.com wrote: On Wed, Mar 4, 2009 at 12:28 AM, Nicolas nsa...@ucalgary.ca wrote: Manik Mayur a écrit : On Tue, Mar 3, 2009 at 11

Re: [gmx-users] Problem configuring openMPI

On Wed, Mar 4, 2009 at 1:18 AM, Roland Schulz rol...@utk.edu wrote: you will have to set LD_LIBRARY_PATH to /home/openmpi/lib I have tried that.. the error still persists. use either setenv or export depending on your shell Roland On Tue, Mar 3, 2009 at 2:35 PM, Manik Mayur manik.ma

Re: [gmx-users] Problem configuring openMPI

, as for now, its working to my need. But somehow still I feel that with openmpi-1.3, gromacs-4.0.4 and Xeon Quad core at 3.6Ghz, the processing speed which I am getting, is quite low. You still have references to lam in your libmd_mpi.so Roland On Tue, Mar 3, 2009 at 3:03 PM, Manik Mayur manik.ma

Re: [gmx-users] Problem configuring openMPI

On Wed, Mar 4, 2009 at 2:25 AM, Mark Abraham mark.abra...@anu.edu.auwrote: Manik Mayur wrote: On Wed, Mar 4, 2009 at 1:55 AM, Roland Schulz rol...@utk.edu mailto: rol...@utk.edu wrote: You will have to recompile everything: make clean make I tried that but to no avail

Re: [gmx-users] Interpretation of g_hbond results

On Tue, Feb 24, 2009 at 9:44 PM, Justin A. Lemkul jalem...@vt.edu wrote: Hi, I have a quick question about interpreting the output from g_hbond. I am using the -ac option to calculate H-bond lifetimes between my protein and a series of different, bound ligands. I read the associated

Re: [gmx-users] problem in running gromacs

? Read http://www.gromacs.org/mailing_lists/users.php -Manik Mayur -- Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] problem in gromacs installation

On Fri, Feb 20, 2009 at 2:45 PM, nitu sharma sharmanit...@gmail.com wrote: Dear All, I have successfully insstalled gromacs on my 32 bit i686 linux system but when I give the mdrun command for running gromacs on my system the output is like this mdrun: error while

Re: [gmx-users] problem in gromacs installation

On Thu, Feb 19, 2009 at 10:45 AM, nitu sharma sharmanit...@gmail.comwrote: *Dear All, I have compiled fft-3.2.1 in a specific user directory; then configured, compiled gromacs-4.0.3 from source code according to directions and installed it in the specific directory, all without any errors,

[gmx-users] genion and a few other problems

Hi all, I have a few probIems/confusions and will be extremely thankful for any help. I added some Cl- ions by replacing water using genion (and -nn). It generated a topol.top file with Cl listed in [ molecules ]. Now when I try to run grompp, it gives an error saying no such molecule type Cl. So

[gmx-users] Re: genion and a few other problems

On Sat, Dec 27, 2008 at 3:12 PM, Manik Mayur manik.ma...@gmail.com wrote: Hi all, I have a few probIems/confusions and will be extremely thankful for any help. I added some Cl- ions by replacing water using genion (and -nn). It generated a topol.top file with Cl listed in [ molecules ]. Now

Re: [gmx-users] Re: genion and a few other problems

On Sat, Dec 27, 2008 at 6:36 PM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Manik Mayur manik.ma...@gmail.com: On Sat, Dec 27, 2008 at 3:12 PM, Manik Mayur manik.ma...@gmail.com wrote: Hi all, I have a few probIems/confusions and will be extremely thankful for any help. I

[gmx-users] partial charge distribution

Hi, I have a system (a slit type nanopore) in which I have 4 wall layers. I would like to distribute partial charges on the first wall layer (the layer in contact with the fluid). The wall layers are made of Si atoms. I tried to change ffG43a1nb.itp ( ffG43a1.atp) by adding a new atom with

Re: [gmx-users] Parallel run on a Quad Core

On Sun, Dec 21, 2008 at 5:04 PM, Chitrita Dutta Roy chitrita...@gmail.comwrote: Thanks to all for helping me previously. Now i am unable to arrange the .tpr file for position restraint mdrun on a quad core as in version 4.0.2 grompp -np is not a valid comand can anybody help me in building a

Re: [gmx-users] Gromacs 4 with mpi interface

I am not sure that mdrun_mpi or for that matter mdrun with options -np 2 -multi 1 (I have a core 2 duo machine) is actually running the process parallely, as the estimated time for completion for a simulation is the same as without. I have built open-mpi library, so do I have to make some changes

[gmx-users] Tau_t error

Hi, I am trying to remove thermostat on a certain group of atoms by taking tau_t = 0. But upon using grompp it says: For proper thermostat integration tau_t (0) should be more than an order of magnitude larger than delta_t. And gives a warning. This was not there in v3.3. Is this a bug or should

[gmx-users] COMM and WCA

Hi, I was wondering if there is any way to: 1) COMM removal in a specific dimension just life freezedim. e.g. I want COMM removal in y-direction only. 2) Get WCA potential by setting [vdw-type: Shift] and [rvdw=2^(1/6)*sigma]; As in WCA the repulsive part of LJ is retained by setting the cutoff

[gmx-users] Re: gmx-users Digest, Vol 56, Issue 39

list for GROMACS users gmx-users@gromacs.org Message-ID: 49418d58.9010...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Manik Mayur wrote: Hi, I am trying to remove thermostat on a certain group of atoms by taking tau_t = 0. But upon using grompp it says

[gmx-users] COMM removal and thermostat

size of COMM removal and Tau_t of the thermostat? Thanks, Manik Mayur -- _ HAPAX LEGOMENA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http