[gmx-users] Bond energy doesn't appear in gromacs rerun

Hello everyone, I am doing single point energy calculation for a certain configuration of a molecule using rerun option of gromacs. But in the energy output, there is no Energy term related to BOND.  Do you know why? Thanks Golshan -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k

Hello, I have performed quit a lot of tests and I have some question: I have an amber.crd and amber.top files ... I perform a single step energy calculation with amber , gromacs and cp2k. in all of them I am using amber force field but the point is that in cp2k and amber, I am reading crd and

Re: [gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k

: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, August 8, 2013 2:40 AM Subject: Re: [gmx-users] BOND ... ANGLE and TORSION energy discrepancy between gromacs and cp2k On 2013-08-08 01:16, Golshan Hejazi wrote: Hello, I

[gmx-users] CGennFF in gromacs

Hello everyone, I want to use CGennFF force field in GROMACS. I downloaded the Cgenffbon.itp and  Cgenffnb.itp files and I put them in charmm36.ff directory.  - I replaced the lines in the forcefield.itp to #include Cgenffbon.itp  and #include Cgenffnb.itp  - I modified the rtp file and I

[gmx-users] adding ETHANOL to CGennFF in gromacs has problem

Hello, I am trying to add ethanol as a new residue to CGenFF force field in gromacs. Basically, I need to bring this information from charmm rtf file to the gromacs format. This is the information taken from rtf file of charmm. RESI ETOH          0.00 ! C2H6O Ethanol, adm jr. GROUP ATOM C1  

Re: [gmx-users] adding ETHANOL to CGennFF in gromacs has problem

for GROMACS users gmx-users@gromacs.org Sent: Monday, September 2, 2013 1:34 PM Subject: Re: [gmx-users] adding ETHANOL to CGennFF in gromacs has problem Please make sure to keep the discussion on the mailing list. On 9/2/13 1:27 PM, Golshan Hejazi wrote: This is the gro file that I am using

[gmx-users] simulation explode while switching from NVT to NPT

Hi everyone, I am simulating a system of paracetamol crystal in ethanol solvent. I used pdb2gmx to generate the topology and gro file and I minimized the system using steepest decent. As long as I perform NVT simulations at any temperature, the simulations goes on! But as soon as I switch from

Re: [gmx-users] simulation explode while switching from NVT to NPT

simulation at 20K and another 5ns at 50K. But still as soon as I turn on the barostate ... the simulation crashes. Do you have any other suggestion? Thanks G. From: Rafael I. Silverman y de la Vega rsilv...@ucsc.edu To: Golshan Hejazi golshan.hej...@yahoo.com

[gmx-users] ERROR while compiling gromacs4.6.1

Hello, i am trying to compile gromacs-4.6.1 on a linux machine. I used already the following compile script and it worked export CCDIR=/usr/bin/gcc export MPICCDIR=/usr/mpi/gcc/openmpi-1.4.1/bin export CXX=mpicxx export CC=mpicc cd /home/fbafti/CODE tar -xvf gromacs-4.6.1.tar.gz cd mv