[gmx-users] internal consistency warning in grompp not repeated at end of stderr output

I recently generated a new .top file and I accidentally missed the first line in the water position restraint section while pasting. Therefore I had water posre without wanting it. First of all, I would like to point out that the gromacs error-checking is excellent since it was aware of this e

Re: [gmx-users] benchmark numbers

vipin sachdeva wrote: Woodcrest runs a 64 bit OS and compiles natively to a 64 bit binary. I am 2X slow, for instance the PPC 970 1600 mhz with 512 Kb L2 Cache (Mine is 2000 mhz dual-chip with 512 Kb each with one core disabled) gcc number for d.villin is 9443 ps/day == 9.443 ns/day. For me

Re: [gmx-users] benchmark numbers

Woodcrest runs a 64 bit OS and compiles natively to a 64 bit binary. I am 2X slow, for instance the PPC 970 1600 mhz with 512 Kb L2 Cache (Mine is 2000 mhz dual-chip with 512 Kb each with one core disabled) gcc number for d.villin is 9443 ps/day == 9.443 ns/day. For me the number printed at

Re: [gmx-users] benchmark numbers

vipin sachdeva wrote: Yes, I am really off (more than 2X for both Woodcrest and PPC970). I was earlier doing the configure flags CC=gcc CFLAGS=-O3 LDFLAGS=-O3 --enable-ppc-altivec (--enable-x86-64-sse) --enable-cpu-optimizations --enable-float --disable-threads (single node results) only.

Re: [gmx-users] benchmark numbers

Also, the flag --with-fft=fftw3 was also used. ( with appropriate CPPFLAGS and LDFLAGS). On Mon, 9 Apr 2007, vipin sachdeva wrote: Yes, I am really off (more than 2X for both Woodcrest and PPC970). I was earlier doing the configure flags CC=gcc CFLAGS=-O3 LDFLAGS=-O3 --enable-ppc-altive

Re: [gmx-users] benchmark numbers

Yes, I am really off (more than 2X for both Woodcrest and PPC970). I was earlier doing the configure flags CC=gcc CFLAGS=-O3 LDFLAGS=-O3 --enable-ppc-altivec (--enable-x86-64-sse) --enable-cpu-optimizations --enable-float --disable-threads (single node results) only. and I found I was 2X of

Re: [gmx-users] gromos

Ashish Gupta wrote: Hello gmx-users, I came across GROMOS MD software (http://www.igc.ethz.ch/gromos/index.html) Is this software similar to GROMACS MD software? Will going through GROMOS manual help me gain some further insights into GROMACS. Not likely, but please be more specific. If y

[gmx-users] gromos

Hello gmx-users, I came across GROMOS MD software (http://www.igc.ethz.ch/gromos/index.html) Is this software similar to GROMACS MD software? Will going through GROMOS manual help me gain some further insights into GROMACS. Also, I found from the gromos website that the manual has som

Re: [gmx-users] benchmark numbers

vipin sachdeva wrote: Hi, I am trying to reproduce the benchmark numbers for PPC970 and the Woodcrest. There is no listing, that I could find, which details the compiler options (configure options), or other details that could help reproduce the numbers. If someone could provide more info

[gmx-users] benchmark numbers

Hi, I am trying to reproduce the benchmark numbers for PPC970 and the Woodcrest. There is no listing, that I could find, which details the compiler options (configure options), or other details that could help reproduce the numbers. If someone could provide more info on the compiler flags

Re: [gmx-users] how to submit replica exchange MD simulation

N-J.M. Macaluso wrote: Hello, I have a question regarding replica exchange MD in Gromacs. I think I am preparing all of the files in the correct fashion, but I continually get the same error message. Here is what I'm doing. I prepared three different mdp files, each specifying a specifi

[gmx-users] how to submit replica exchange MD simulation

Hello, I have a question regarding replica exchange MD in Gromacs. I think I am preparing all of the files in the correct fashion, but I continually get the same error message. Here is what I'm doing. I prepared three different mdp files, each specifying a specific temperature (PME0.mdp,