RE: [gmx-users] mdrun-gpu error

Hi Renato, Fatal error: reading tpx file (md.tpr) version 73 with version 71 program This error occur because you are using different version of the gromacs. Are you sure that the version of the grompp is the same of the mdrun I hope this help. Prof. Dr. Osmair V. Oliveira Federal Institute

RE: [gmx-users] Dipeptide generation problem [Justin]

Hi Eudes, I do not know how work CHARMM force field, but if you use the following PDB file for your dipeptide using OPLS-AA force field, you can obtain good results!. ATOM 1 N PHE 1 0.000 0.000 0.000 1.00 0.00 ATOM 2 H1 PHE 1 -0.940 0.000 -0.330 1.00

RE: [gmx-users] Epsilon AA, Epsilon AB, Epsilon BB

If you will use Lennard-Jones potential, you can combine both epsilons: AB = sqrt(AA*BB) Osmair Date: Tue, 24 Aug 2010 15:48:56 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Epsilon AA, Epsilon AB, Epsilon BB Rohit Malshe wrote: Dear all, I

RE: [gmx-users] Finding H-Bond donor-acceptor pairs

Hi Anirban, Use g_hbond with -g option. -) Osmair Date: Thu, 14 Jan 2010 13:54:09 +0530 From: reach.anirban.gh...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Finding H-Bond donor-acceptor pairs Hi ALL, I was just wondering if GROMACS has any tool to list out the hydrogen bond

[gmx-users] Hard sphere simulation

Hi, I would like to simulate hard sphere with different charge values (e.g. +30), with different diameters (e.g. 5 nm) and with different values of Lennard-Jones. In addiction, in these models of the hard sphere I would like to insert dipole (e.g. 15 Debye). So, is this possible to simulate

[gmx-users] Install gromacs333 with plumed110

Hi, I am trying to install gromacs 3.3.3 with plumed 1.1.0 with the following commands: $ export plumedir=/home/osmair/programs/PLUMED-1.1.0 $ CC=gcc CXX=g++ ./configure --enable-double --program-suffix=_plumed --enable-fortran --enable-mpi CPPFLAGS=-I/home/osmair/programs/fftw-3.0.1/include

RE: [gmx-users] How to fi all atoms and to calculate the energy

Hi Luis, If you want only the initial energy, you can try minimize your system using gradient conjugate (cg) or steepest descent (steep) algorithm with large value of tolerance (emtol). Of course, using steeps of MD from GROMACS. I hope this help. Ph.D. Osmair V. Oliveira Federal University of

RE: [gmx-users] Nanoparticles does not interact

2009 12:12:34 +1000 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] Nanoparticles does not interact osmair oliveira wrote: My *.top file is: #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl CeO 3 [ atoms ] ; nr

[gmx-users] Nanoparticles does not interact

Hi, I have minimized four nanoparticle (with 0.5 nm of distance) using the oplsaa force field, but the output (*.edr) shows that the interactions (Coul-SR and LJ-SR) between the nanoparticles are zero, as example: Coul-SR:1CeO-1CeO 5.84835e+04 5.43362e+09 4.45364e+06

RE: [gmx-users] Nanoparticles does not interact

My *.top file is: #include ffoplsaa.itp [ moleculetype ] ; Namenrexcl CeO 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1opls_966 1 CeO O 1 -0.5000 15.9994 53 opls_967 1 CeO Ce 2 1. 140.116 [ bonds ] 53 1 1 ... [ angles ]

RE: [gmx-users] Combining LJ and buckingham potential

the [ nonbond_params ] [ pairs ] sections of the TOP file? How did you define these interactions in your TOP file? --Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Fri, Apr 17, 2009 at 22:51, osmair oliveira osmai...@hotmail.com wrote

[gmx-users] Combining LJ and buckingham potential

Hi, I have tried to simulate a crystal in water solvent, however I found the error: ERROR 0 [file new-topol3.top, line 19]: Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR) So, my question: How can I use or define LJ potential (for water) and buckingham potential (for a

RE: [gmx-users] Problem using MPIRUN MDRUN

Hi Filippo, Do you have checked your trajectory ( *.trr or *.xtc) and *.log ? You system may have 'exploded'... Osmair Date: Fri, 13 Feb 2009 13:27:09 + From: fpri...@nimr.mrc.ac.uk To: gmx-users@gromacs.org Subject: [gmx-users] Problem using MPIRUN MDRUN Dear users, I'm trying

[gmx-users] QMMM/mopac install

Hi, I am trying to install gromacs333 with mopac. I use the command: ./configure --enable-mpi --with-qmmm-mopac CPPFLAGS=-DUSE_MOPAC LDFLAGS=-L/home/osmair/qmmm/ -LD_LIBRARY_PATH=-lmopac However I found the following error when I run make: mpicc -O3 -fomit-frame-pointer -finline-functions

RE: [gmx-users] QMMM/mopac install

`/home/osmair/qmmm/pack-gromacs-3.3.3-meta/src' make: *** [all-recursive] Error 1 Osmair Date: Fri, 6 Feb 2009 13:18:28 -0500 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] QMMM/mopac install osmair oliveira wrote: mpicc: No such file or directory It appears