[gmx-users] Pull code grompp error

2017-03-24 Thread Souparno Adhikary
ked. Regards, Souparno Adhikary University of Calcutta, India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests vi

[gmx-users] FSync error

2017-03-24 Thread Souparno Adhikary
help to indicate what might be the problem? Thanks, Souparno Adhikary, University of Calcutta, India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support

[gmx-users] Pull Code constant value

2017-03-28 Thread Souparno Adhikary
this value or it simply based on the trial-and-error method? Also, what problems can take place if the value is large (huge, I guess)? Thanks, Souparno Adhikary University of Calcutta. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Secondary structure analysis

2017-03-26 Thread Souparno Adhikary
I think dssp is a useful tool for this purpose... Souparno On 26 Mar 2017 19:50, "Justin Lemkul" wrote: > > > On 3/26/17 8:21 AM, RAHUL SURESH wrote: > >> I use gromacs 2016.1 version. How to do secondary structure analysis ? >> >> >

Re: [gmx-users] calculation of self energy of protein

2017-03-26 Thread Souparno Adhikary
Do you mean the potential energy of the protein? On 26 Mar 2017 14:24, "Saumyak Mukherjee" wrote: > Dear Users, > > How can the self energy of a protein be calculated from GROMACS. This means > that I want only the inherent energy of the protein, excluding the >

Re: [gmx-users] Pull code grompp error

2017-03-24 Thread Souparno Adhikary
out making an index file, just putting the name of the molecules? Thanks, Souparno On Fri, Mar 24, 2017 at 1:03 PM, Tasneem Kausar <tasneemkausa...@gmail.com> wrote: > Define you pull group in index file as the error message says. > > On Fri, Mar 24, 2017 at 12:18 PM, So

Re: [gmx-users] FSync error

2017-03-24 Thread Souparno Adhikary
ow > that. By the way, 4.5.6 is prehistoric - please update for faster > simulations, more chance of people being able to help you, and fewer bugs! > > Mark > > On Fri, 24 Mar 2017 09:34 Souparno Adhikary <souparno...@gmail.com> wrote: > > > I'm getting the followi

[gmx-users] No data on Pullf and Pullx files after restart

2017-04-04 Thread Souparno Adhikary
Hello, I restarted my umbrella sampling simulations using the tpbconv command. I used the -vel option in the command. It ran successfully. After that, when I am running the new simulations, pullf and pullx files are created for each sample but no data gets written in them. I am absolutely

[gmx-users] Nucleic Acid in GROMOS54A7

2017-07-31 Thread Souparno Adhikary
Hi all, I was trying to simulate a protein-DNA complex using gromos54a7 forcefield. The error comes as, Fatal error: Residue 'DA' not found in residue topology database Clearly, it is not finding the DA residue in its database. How can I solve this? Thanks, Souparno Adhikary, CHPC Lab

[gmx-users] (no subject)

2017-07-31 Thread Souparno Adhikary
Hi all, I was trying to simulate a protein-DNA complex using gromos54a7 forcefield. The error comes as, Fatal error: Residue 'DA' not found in residue topology database Clearly, it is not finding the DA residue in its database. How can I solve this? Thanks, Souparno Adhikary, CHPC Lab

Re: [gmx-users] Using external force field with GROMACS

2017-07-31 Thread Souparno Adhikary
. How can we specifically mention GROMACS 5.1.4 to work with the new forcefield files? Thanks, Souparno Adhikary, CHPC Lab, Department of Microbiology, University of Calcutta. On Fri, Jul 28, 2017 at 2:29 PM, Qinghua Liao <scorpio.l...@gmail.com> wrote: > Hello, > > You

Re: [gmx-users] Nucleic Acid in GROMOS54A7

2017-07-31 Thread Souparno Adhikary
DA is the Adenine residue. It goes fine with other forcefields like CHARMM27 and AMBER99 SBILDN. In my knowledge, there's no problem in the parameters. Souparno Adhikary, CHPC Lab, Department of Microbiology, University of Calcutta. On Mon, Jul 31, 2017 at 3:43 PM, Mark Abraham <mark.j.a

[gmx-users] Using external force field with GROMACS

2017-07-28 Thread Souparno Adhikary
- 4.5.6 (I don't know why they are not eager to update it). Thanks, Souparno Adhikary, CHPC Lab, Department of Microbiology, University of Calcutta. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

[gmx-users] Error with MPICH

2017-08-18 Thread Souparno Adhikary
on the internet suggested, I recompiled the mpich with --enable-shared option and also setting the CXXFLAGS as -fPIC. It still doesn't work. Can you please help? Souparno Adhikary, CHPC Lab, Department of Microbiology, University of Calcutta. -- Gromacs Users mailing list * Please search

Re: [gmx-users] Error with MPICH

2017-08-18 Thread Souparno Adhikary
My CMAKE was like this: /root/cmake-3.9.1-Linux-x86_64/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.1.4 I have compiled mpich2 with --enable-shared option. Souparno Adhikary, CHPC Lab, Department of Microbiology

[gmx-users] Coordinates not matching with topology file

2017-09-14 Thread Souparno Adhikary
[ system ] molecule in water [ molecules ] DRG 1 SOL 11200 We are absolutely clueless from where it is computing the 33698 atoms in the topology file. We tried adjusting the number of atoms manually but went in vain. Can you please help us??? Souparno Adhikary, CHPC L

[gmx-users] Blank Coordinate File

2017-09-18 Thread Souparno Adhikary
have a choice: You can make one point or no points." (Paul Sigler) Any help??? Please??? Souparno Adhikary, CHPC Lab, Department of Microbiology, University of Calcutta. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List befo

[gmx-users] gmx insert-molecules not inserting molecules

2017-09-13 Thread Souparno Adhikary
to g1new.gro Output configuration contains 33766 atoms in 11201 residues What could be the possible problem??? We used the gmx insert-molecules as: gmx insert-molecules -f mol1wt.gro -ci mol1_op.gro -o mol1new.gro -nmol 4 Souparno Adhikary, CHPC Lab, Department of Microbiology, University

Re: [gmx-users] MPICH2 error

2017-08-21 Thread Souparno Adhikary
Okay, it worked. After I put on -DCMAKE_C_COMPILER and -DCMAKE_CXX_COMPILER in my configuration options. Thanks. Souparno Adhikary, CHPC Lab, Department of Microbiology, University of Calcutta. On Mon, Aug 21, 2017 at 5:04 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi,

Re: [gmx-users] MPICH2 error

2017-08-21 Thread Souparno Adhikary
I am using MPI compilers to do the thing. I reinstalled MPICH2 using the options and it looks the same. Sorry... Souparno Adhikary, CHPC Lab, Department of Microbiology, University of Calcutta. On Mon, Aug 21, 2017 at 4:08 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, >

[gmx-users] MPICH2 error

2017-08-21 Thread Souparno Adhikary
value collect2: ld returned 1 exit status make[2]: *** [lib/libgromacs_mpi.so.1.4.0] Error 1 make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 make: *** [all] Error 2 Can anyone please help??? Souparno Adhikary, CHPC Lab, Department of Microbiology, University of Calcutta

[gmx-users] GROMACS with Torque: Job stuck

2017-08-25 Thread Souparno Adhikary
up GROMACS with Torque. I compiled GROMACS with -DGMX_MPI=ON The nodes file is not written and the job stays stuck. Can anyone familiar with job scheduling help me in this regard??? Souparno Adhikary, CHPC Lab, Department of Microbiology, University of Calcutta. -- Gromacs Users mailing l

Re: [gmx-users] GROMACS with Torque: Job stuck

2017-08-25 Thread Souparno Adhikary
. Even, at every node, mpi and GROMACS are installed in the same location i. e. /usr/local/ I tried running simple "echo" jobs and they are running successfully. That's why it seems to me that it might be a problem with integrating GROMACS. Souparno Adhikary, CHPC Lab, Department of Mi

[gmx-users] Water molecule error

2017-11-07 Thread Souparno Adhikary
pdb files with previous and current coordinates ^Mstep 0 WARNING: Listed nonbonded interaction between particles 6528 and 6537 at distance 2.910 which is larger than the table limit 2.232 nm. Can you please suggest what can I do to fix this? Souparno Adhikary, CHPC Lab, Department of Microbiology, U

[gmx-users] Pulling protein from distance on membrane

2018-02-13 Thread Souparno Adhikary
on the protein to make it go away from the membrane, I have successfully found the experimental results. Now, I want to put the protein from outside the membrane (as the phenomenon takes place in the in vitro system). Thanks in advance, Souparno Adhikary, CHPC Lab, Department of Microbiology, University