Re: [gmx-users] total simulation time for proteins in general

Hi, On Apr 11, 2007, at 7:26 AM, Priya Chandran wrote: 2. Is minimisation in GROMACS only used as a precursor to the md- simulation to remove bad contacts, or can we also use it effectively to minimize a raw modelled ab-initio structure.? Well, technically you can of course use it, but any

Re: [gmx-users] BHIS for HIS?

Hi, pdb2gmx tries to choose the HIS protonation based on hydrogen bond patterns in the structure, so unless you are absolutely certain you need the alternative state you should need to do anything. In the latter case, just edit the name in the PDB file (to HISB or HISH) prior to running p

Re: [gmx-users] --enable-threads fails.

Hi, The prefetching hardware is pretty good at hiding latencies, but obviously you'll get better performance when everything fits in cache. However, the largest data structures by far are the neighborlists, and their _total_ size for the simulation is independent of whether you are using

Re: [gmx-users] total simulation time for proteins in general

Priya Chandran wrote: Hello, I am a beginner in GROMACS and I am using GROMACS to analyse the solution structure of protein in water after initial homology/abinitio modelling. I have already run a search on the gmx_users list for my queries. There are a few basic questions i would like to ask.

[gmx-users] total simulation time for proteins in general

Hello, I am a beginner in GROMACS and I am using GROMACS to analyse the solution structure of protein in water after initial homology/abinitio modelling. I have already run a search on the gmx_users list for my queries. There are a few basic questions i would like to ask. 1. In the md integrator

Re: [gmx-users] BHIS for HIS?

Hi Rongliang Wu, You could try to get your hands on a GROMOS manual... Alternatively, draw the histidines using the information in the rtp files. Alternatively, take a histidine, run it through pdb2gmx with -his and try all options. Histidine has different protonation states, and one of the histi

Re: [gmx-users] small molecules simulation

Hi, > > Back Off! I just backed up run.xtc to ./#run.xtc.1# > step 90, remaining runtime: 161 s Section mistake Hmmm I've never seen that error before. That is not a Gromacs error message (as confirmed by a check of the source code). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD

[gmx-users] BHIS for HIS?

hello,gmx-users， i am trying to simulate a peptide with residue HIS, the default in pdb2gmx used HISB for HIS in both oplsaa and gromos96 force field, but i found there are HIS1,HISH,HISB etc in the rtp files, i am not sure whether HISB will suffice for my system, i intend to simulate th

Re: [gmx-users] Running multiple kernels

Hi, On Apr 10, 2007, at 9:11 PM, Justin M. Shorb wrote: Greetings, I have been running a modified version of gromacs 3.3 and would like to run two kernel loops: one which is 330 and one which is 300. In the src/gmxlib/nonbonded/nb_kerneltype.h file it strictly says to use wrapper routine

Re: [gmx-users] --enable-threads fails.

Thanks. Do you see L2 cache overflowing effects by putting multiple MPI processes on the same chip with the recent multi-core processors (Intel Woodcrest for instance)? Regards vipin On Tue, 10 Apr 2007, Erik Lindahl wrote: Hi, On Apr 10, 2007, at 10:15 PM, vipin sachdeva wrote: Thi

Re: [gmx-users] --enable-threads fails.

Hi, On Apr 10, 2007, at 10:15 PM, vipin sachdeva wrote: This thread on Feb 8 2006 mentions that threads are not yet functional. http://www.gromacs.org/pipermail/gmx-users/2006-February/019760.html Is the threads still not functional considering I still get the same error ? We are only

[gmx-users] Running multiple kernels

Greetings, I have been running a modified version of gromacs 3.3 and would like to run two kernel loops: one which is 330 and one which is 300. In the src/gmxlib/nonbonded/nb_kerneltype.h file it strictly says to use wrapper routines that are included in the gmx_nonbonded.h file, which I cann

Re: [gmx-users] --enable-threads fails.

vipin sachdeva wrote: This thread on Feb 8 2006 mentions that threads are not yet functional. http://www.gromacs.org/pipermail/gmx-users/2006-February/019760.html Is the threads still not functional considering I still get the same error ? correct. won't be for a while. Regards vipin _

[gmx-users] --enable-threads fails.

This thread on Feb 8 2006 mentions that threads are not yet functional. http://www.gromacs.org/pipermail/gmx-users/2006-February/019760.html Is the threads still not functional considering I still get the same error ? Regards vipin ___ gmx-users

Re: [gmx-users] Woodcrest results

Yes, they are fine now; I guess it was just confusion. Thanks for the help. Regards vipin On Tue, 10 Apr 2007, David van der Spoel wrote: vipin sachdeva wrote: Considering that you are running 4 MPI processes on 4 cores/2 chips system, don't you think the title of the page of the benc

Re: [gmx-users] Woodcrest results

vipin sachdeva wrote: Considering that you are running 4 MPI processes on 4 cores/2 chips system, don't you think the title of the page of the benchmarks is misleading -- "Single processor benchmarks" ? Also, won't we get better performance with running threads. I believe the 2 chips are co

Re: [gmx-users] Woodcrest results

Considering that you are running 4 MPI processes on 4 cores/2 chips system, don't you think the title of the page of the benchmarks is misleading -- "Single processor benchmarks" ? Also, won't we get better performance with running threads. I believe the 2 chips are connected through a fron

Re: [gmx-users] small molecules simulation

root wrote: Hello everyone,today I tried to simulate several small molecules, however I failed. The process is like this: Thank you for describing your process. This makes it much easier to help you. I got DRG.gro and DRG.itp files from the PRODRG website, and used the command "genbox" to o

Re: [gmx-users] Woodcrest results

vipin sachdeva wrote: So on the single processor page, the results are mentioned for woodcrest, which had 4 physical cores. I want to confirm that the results are by running 4 threads rather than 1 thread? Also the cache mentioned is 6 MB. Is that per 2 cores or for all the 4 cores ? Since

[gmx-users] Woodcrest results

So on the single processor page, the results are mentioned for woodcrest, which had 4 physical cores. I want to confirm that the results are by running 4 threads rather than 1 thread? Also the cache mentioned is 6 MB. Is that per 2 cores or for all the 4 cores ? Regards vipin __

[gmx-users] small molecules simulation

Hello everyone,today I tried to simulate several small molecules, however I failed. The process is like this: I got DRG.gro and DRG.itp files from the PRODRG website, and used the command "genbox" to obtain a random listed conf.gro of 33 phenol molecules. Then I include "ffgmx" and " DRG.ITP” to g

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

this actually seems to be a message from cpp, therefore it is not counted in the normal warning system. Unless we implement our own baby-cpp it will be quite tedious to catch the warnings and error messages from it. That makes sense. Thanks for the advice. In any event I should get back into

Re: [gmx-users] calculating properties of polyaromatics using gromacs

Hi Fredrik, Basically, you don't (you can't in any case run it on something not in the database). pdb2gmx is designed to build topologies for proteins/dna. There are some more building blocks, and you can add your own, if required. If you mean polyaromatic in terms of a polymer of an aromatic bui

[gmx-users] calculating properties of polyaromatics using gromacs

Dear All I am a new user of Gromacs which means I am in the (somewhat painful) process of learning how to use the program. My goal is to calculate properties for polyaromatics containing nitrogen and sulfur. I want to use a united atom force field and if I have understood it correctly I should

Re: [gmx-users] energy

mahbubeh zarrabi wrote: Dear all I am trying to calculate the binding free energy of protein and ligand, I used the g_lie command but lie.xvg=0 .what is wrong? thanks have you read the papers from the Aqvist group? _

[gmx-users] energy

Dear all I am trying to calculate the binding free energy of protein and ligand, I used the g_lie command but lie.xvg=0 .what is wrong? thanks Finding fabulous fares is fun. Let Yahoo! FareChase search

Re: [gmx-users] Compile Gromacs for Blue Gene/L

Hi Eric, I think you'll be _very_ happy with Gromacs4, or the current CVS version if you want to test that :-) One problem is that "relative scaling" is a rather pointless measure, since it will be better the slower the code is on a single CPU (less time spent in communication). Our paral

Re: [gmx-users] g_energy

mahbubeh zarrabi wrote: Dear GROMACS users I want to calculate free energy in complex,receptor and ligand .what are energy groups in md.mdp? protein,solution or protein,protein,solution thanks please read the manual, chapter 3 etc. then look on the gromacs wesbite for tutorials. _

[gmx-users] g_energy

Dear GROMACS users I want to calculate free energy in complex,receptor and ligand .what are energy groups in md.mdp? protein,solution or protein,protein,solution thanks Expecting? Get great news right away with

Re: [gmx-users] MD simulation of 2 molecules in a system

Alif M Latif wrote: Dear GROMACS users, I was wondering if GROMACS can run MD simulation of two molecules in one system (box+spc water). This two molecules have the hydrophobic and polarity effects which i want to see through the simulation. Can anybody suggest how to do it? I cant find it in

Re: [gmx-users] MD simulation of 2 molecules in a system

Alif M Latif wrote: Dear GROMACS users, I was wondering if GROMACS can run MD simulation of two molecules in one system (box+spc water). This two molecules have the hydrophobic and polarity effects which i want to see through the simulation. Can anybody suggest how to do it? I cant find it in

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

Chris Neale wrote: 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

[gmx-users] MD simulation of 2 molecules in a system

Dear GROMACS users, I was wondering if GROMACS can run MD simulation of two molecules in one system (box+spc water). This two molecules have the hydrophobic and polarity effects which i want to see through the simulation. Can anybody suggest how to do it? I cant find it in the manual (or maybe