[gmx-users] Trouble with the command g_x2top

2013-12-12 Thread Felix Weng
Dear all, I had trouble with the command g_x2top while trying to generate the topology file for the molecule SAM. Error came up as followed. Program g_x2top, VERSION 4.5.5 Source code file: g_x2top.c, line: 505 Fatal error: No or incorrect atomname2type.n2t file found (looking for amber94.ff)

Re: [gmx-users] Normal Mode Analysis with Gromacs 4.6

2013-12-12 Thread Mark Abraham
Why are you using PME-switch? Without explicitly choosing a switch? Mark On Thu, Dec 12, 2013 at 6:45 PM, mcfc1301 mcfc1...@gmail.com wrote: Hello Everyone， I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot but find little useful. My Gromacs was installed in a

Re: [gmx-users] pressure based replica exchange

2013-12-12 Thread Mark Abraham
Quite right, sorry. P as the control variable is not implemented. NPT with T as the control variable is, for example. Mark On Thu, Dec 12, 2013 at 5:58 PM, Michael Shirts mrshi...@gmail.com wrote: Pressure replica exchange is not in currently. It will be added eventually (it's not that hard,

Re: [gmx-users] pressure based replica exchange

2013-12-12 Thread Thomas Evangelidis
I'm not sure if pressure-based REMD is possible, but PLUMED-2.0 provides a quite flexible implementation of Hamiltonian REMD for GROMACS. It may be worth-checking it: http://arxiv.org/abs/1307.5144 On 12 December 2013 12:11, Mark Abraham mark.j.abra...@gmail.com wrote: Quite right, sorry. P

Re: [gmx-users] pressure based replica exchange

2013-12-12 Thread Jianguo Li
Thanks Michael and Mark. Implementation of the pressure based replica exchange will be useful for membrane systems as membranes will be unstable using temperature based replica exchange. Btw, I noticed there is a recent paper on surface tension replica exchange simulations of membranes:

Re: [gmx-users] editconf and conect option

2013-12-12 Thread Steve
Thanks for your response. When I used the tpr file it DID work. When I tried the pdb file here is the error message I got: Program editconf, VERSION 4.5.4 Source code file: tpxio.c, line: 1970 Fatal error: Can not read file 50ps.pdb, this file is from a Gromacs version which is

[gmx-users] Running gromacs 4.6.5 on BGQ

2013-12-12 Thread didymos
Hi, I installed the newest version of gromacs on BGQ: I used these options for whole installation cmake -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=$HOME/gromacs-4.6.5/ -DGMX_DOUBLE=ON -DCMAKE_PREFIX_PATH=$HOME/fftw/ .. and this option for mdrun installation: cmake -DGMX_MPI=ON

Re: [gmx-users] Pressure coupling constants

2013-12-12 Thread Michael Shirts
The most physical thing would be to prepare a system in a small NVT box, then make the box bigger along one dimension, then do an NVT simulation of that system and see what happens along that dimension over time. Barostats are simply not designed to do nonequilibrium right. They magically create

Re: [gmx-users] Pressure coupling constants

2013-12-12 Thread kpsanto
guess that right! but why do you think NVT scaling of velocities is physical which should also affect the non-equilibrium expansion process? thanks in advance Santo - K. P. Santo Post doctoral fellow Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill, NC, USA --

Re: [gmx-users] Pressure coupling constants

2013-12-12 Thread Michael Shirts
You're right, NVE would probably be better! Otherwise, you would not get expansionary cooling. On Thu, Dec 12, 2013 at 7:08 PM, kpsanto santo...@gmail.com wrote: guess that right! but why do you think NVT scaling of velocities is physical which should also affect the non-equilibrium expansion