Re: [gmx-users] restarting a run using tpbconv

I noticed the time provided was: tpbconv -s protein.tpr -f protein.trr -o protein2.tpr -time -1300 I'd have thought Gromacs would have provided an error if this were the case, but it may be that it's taken the frame closest to the (negative) time requested, and consequently just removing the minu

Re: [gmx-users] Parallel Gromacs Benchmarking with Opteron Dual-Core & Gigabit Ethernet

Hi, On Jul 22, 2007, at 6:08 PM, Kazem Jahanbakhsh wrote: mpirun -np 8 mdrun_d -v -deffnm grompp First, when you run in double precision you will communicate exactly twice as much data. Since gigabit ethernet is usually both latency and bandwidth-limiting, you might get better scaling (a

[gmx-users] Parallel Gromacs Benchmarking with Opteron Dual-Core & Gigabit Ethernet

Dear gmx users, I have accommodated a Linux Cluster consisting of 8 nodes with the following specification: Node HW: Two Dual-Core Opteron 2212 (2GHz + 1 MB cache every core), which means totally 4 cores on every node + 2GByte RAM + Gigabit Eth NICs. Network Infrastructure: Gi

Re: [gmx-users] CVS code needed

Dear Erik, Thank you for the link Kumar On 7/22/07, Erik Lindahl <[EMAIL PROTECTED]> wrote: I put a recent copy (friday) at http://lindahl.sbc.su.se/outgoing/aatto/ Cheers, Erik And yes... we should get a nightly-snapshot system running... :-) On Jul 22, 2007, at 4

Re: [gmx-users] CVS code needed

I put a recent copy (friday) at http://lindahl.sbc.su.se/outgoing/aatto/ Cheers, Erik And yes... we should get a nightly-snapshot system running... :-) On Jul 22, 2007, at 4:08 PM, Kumar V wrote: Hai all, Our campus network is behind firewall because of which I cant use CVS pse

[gmx-users] CVS code needed

Hai all, Our campus network is behind firewall because of which I cant use CVS pserver.. And I dont know any alternative how to get current CVS development code. Can anyone of you tell me how to get gromacs current CVS source code?? I will be grateful even if anyone of u send me tar.gz fi

Re: [gmx-users] wat is the way to solve this prob

David van der Spoel wrote: vijay kumar wrote: what is way to solve this prob Chain identifier '5' was used in two non-sequential blocks (residue 4, atom 4) oh and since this is not a biomolecule, don use pdb2gmx. search the list. your pdb file is a complete mess. it has fixed format. search

Re: [gmx-users] wat is the way to solve this prob

vijay kumar wrote: what is way to solve this prob Chain identifier '5' was used in two non-sequential blocks (residue 4, atom 4) your pdb file is a complete mess. it has fixed format. search internet. don't use tabs only spaces the pdb file is for Si atoms no. of atoms 32 at differeent places

[gmx-users] wat is the way to solve this prob

what is way to solve this prob Chain identifier '5' was used in two non-sequential blocks (residue 4, atom 4) the pdb file is for Si atoms no. of atoms 32 at differeent places ATOM 1 Si.66599000 .66599000 .66599000 ATOM 2 Si 7.30599000 .66599000 .66599000 ATOM