Re: [gmx-users] H2O close to N-terms

On Tue, 2006-06-20 at 11:31 +1000, Mark Abraham wrote: > [EMAIL PROTECTED] wrote: > > > > Someone has written a script to calculate how may times H2O molecules > > get really close or bind to the N-terminals of a protein?(it's outer > > part, not the core) Or maybe someone nows how to calculate

Re: [gmx-users] oplsaa force field and dummy atoms

Yes, I did a detailed search about it. The confusing part is nobody complained about using dummy atoms. Am I missing something? thanks. From: "David Mobley" <[EMAIL PROTECTED]> I think I've seen this one in the archives before. Did you try searching the list? On 6/19/06, MURAT CETINKAYA <[EMAIL

Re: [gmx-users] unexpected result from mdrun

Dongsheng Zhang wrote: Dear David, yes. I have try it. Even I try to give two different name for two tpr file, then COPY them to those directories. Both tpr files in one directory works fine, In the other directory none works. OK, so speaking in an analogy, here we've told the car mechanic ov

Re: [gmx-users] Electrostatic Force Monitoring

Justin M. Shorb wrote: Greetings! I am looking to extract the electrostatic force (non-LJ forces) from an energy monitoring group. Unfortunately, trying to dig into Gromacs source without a map is proving to be quite difficult. Can anyone point me in the direction of the subroutines that hand

Re: [gmx-users] H2O close to N-terms

[EMAIL PROTECTED] wrote: Someone has written a script to calculate how may times H2O molecules get really close or bind to the N-terminals of a protein?(it's outer part, not the core) Or maybe someone nows how to calculate the N-terms interactions with the solvent? Anything related to this wou

Re: [gmx-users] off-diagonal of the tensor for pressure coupling should be zero??

Sunjoo, is there a particular reason why you want to you anisotropic pressure coupling? (I recently tried this myself, on a DMPC bilayer). Some of the key membrane physical properties (like thickness, area per lipid, order parameters) were distorted and did not agree with experimental evidence.

[gmx-users] off-diagonal of the tensor for pressure coupling should be zero??

Dear Gromacs people I am trying to run NPT simulation on a bilayer and want to know right setup to use anisotropic pressure coupling. I have seen two different cases of reference pressure. Some people use 1 atm for off-diagonals (xy, yz, zx directions) but other use 0 atm. From Erik's answer

[gmx-users] H2O close to N-terms

Someone has written a script to calculate how may times H2O molecules get really close or bind to the N-terminals of a protein?(it's outer part, not the core) Or maybe someone nows how to calculate the N-terms interactions with the solvent? Anything related to this would help. __

[gmx-users] afm rate , quick question about units.

Hello, in the GMX manual, on page 117, it states: afm rate1 = afm rate2 = The rate at which the spring moves in *nm/ps* for each group. In my ppa file, I specify: * afm rate1 = 1* But in the log file of my mdrun, it states: Pull rate: 1.00e+00 *nm/ns*. Force constant: 1.00e+03 k

[gmx-users] Electrostatic Force Monitoring

Greetings! I am looking to extract the electrostatic force (non-LJ forces) from an energy monitoring group. Unfortunately, trying to dig into Gromacs source without a map is proving to be quite difficult. Can anyone point me in the direction of the subroutines that handle: - output of the forces

Re: [gmx-users] unexpected result from mdrun

Dear David, yes. I have try it. Even I try to give two different name for two tpr file, then COPY them to those directories. Both tpr files in one directory works fine, In the other directory none works. Dongsheng On Mon, 2006-06-19 at 13:39 -0700, David Mobley wrote: > Maybe they're not exa

Re: [gmx-users] unexpected result from mdrun

Maybe they're not exactly identical? Did you try gmxdump and then diff the output? David On 6/19/06, Dongsheng Zhang <[EMAIL PROTECTED]> wrote: Dear GMX users, I have two EXACTLY identical tpr files at two different directories on the SAME machine. When I try to use these two tpr files. One wo

Re: [gmx-users] unexpected result from mdrun

Dear GMX users, I have two EXACTLY identical tpr files at two different directories on the SAME machine. When I try to use these two tpr files. One works fine. Another one gives me bad result, the molecule explodes. Could anyone tell me why this happens? Thank you in advance! Dongsheng On Mon,

Re: [gmx-users] oplsaa force field and dummy atoms

I think I've seen this one in the archives before. Did you try searching the list? On 6/19/06, MURAT CETINKAYA <[EMAIL PROTECTED]> wrote: Hi GMX users, My question is to calculate solvation free energy of a non-standard residue (I managed to define it into oplsaa database). I followed the tutor

Re: [gmx-users] Fatal error: Shake block crossing node boundaries

Jianwei Wang wrote: Hello, I got an error message while using 8 processors becuase of Shake block crossing node boundaries. Everything was fine when I used a single processor. Any idea how to ease this problem? Thanks! JW use max 3 or 4 processors The error message: splitting to

[gmx-users] unexpected result from mdrun

Dear GMX users, I am studying the interaction between a polymer chain and a nanotube in vacuum. After I set up my system, I use vmd to visualize my gro file. It looks fine. The polymer chain is a little far away from the nanotube. There is no overlap. However, after I do mdrun, I can't get edr fil

Re: [gmx-users] my protein gets cut while preparing for em

On Mon, 19 Jun 2006, Guillem Plasencia wrote: > Then i was curious and did trjconv my system (before running mdrun energy > minimization) into a pdb, and had a look at it, and i saw my protein was > splitted in three different molecules, one was inside the water box (but far > away from box cent

[gmx-users] oplsaa force field and dummy atoms

Hi GMX users, My question is to calculate solvation free energy of a non-standard residue (I managed to define it into oplsaa database). I followed the tutorial prepared by groningen group (http://md.chem.rug.nl/education/Free-Energy_Course/index.html) My problem is how to use dummy atoms in ffop

[gmx-users] Fatal error: Shake block crossing node boundaries

Hello, I got an error message while using 8 processors becuase of Shake block crossing node boundaries. Everything was fine when I used a single processor. Any idea how to ease this problem? Thanks! JW The error message: splitting topology... Walking down the molecule graph to make s

Re: [gmx-users] my protein gets cut while preparing for em

hi, On Monday 19 June 2006 18:06, Guillem Plasencia wrote: > Hello, > > This is my first MD (besides the ones in GROMACS' benchmark), i found the > following problem while following John Kerrigan's tutorial for Drug-Enzyme > complex (the first part, energy minimization), using my own protein and

[gmx-users] pull code questions

Dear all, I had a couple quick questions on the pull code, as I couldn't quite figure this out from the documentation. In particular, I'm interested in the part that does umbrella sampling: 1) If an alternative reference structure is provided to grompp using the -r option (as one would do for po

[gmx-users] GROMACS on parallelknoppìx

I have installed GROMACS compiled with MPI support into the /usr/local directory of ParallelKnoppix. ParallelKnoppix is a Knoppix-like CD that can be used to set up a Linux cluster in about 5 minutes. I have very little experience with GROMACS, but I have run some of the demos, and it looks like

[gmx-users] my protein gets cut while preparing for em

Hello, This is my first MD (besides the ones in GROMACS' benchmark), i found the following problem while following John Kerrigan's tutorial for Drug-Enzyme complex (the first part, energy minimization), using my own protein and its crystallographic ligand i ran into the following: -briefing

RE: [gmx-users] re: need help with free energy of solvation calcu lation

David M., Thanks for the suggestions. About the Yu et al. error bars: > For Yu et > al., the first number is the average from the full 5 ns simulation and > the number in () is for the last 2 ns. If not for the CE23Me case, I would probably assume that the discrepancy due to doing a notorio

Re: [gmx-users] re: need help with free energy of solvation calculation

Jonathan, First, a question: I know that certain values of sc-alpha are preferred for different cases, but are there any values that definitely should not be used? In my calculations, some hydrogens (with charges but no L-J) are mutated into united atom methyls (with charges and L-J), so the

Re: [gmx-users] MPICH or LAM/MPI

Hello, on this note, I'm having issues configuring and installing the mpi enabled mdrun. (see below). I keep getting a strange error: checking size of int... configure: error: cannot compute sizeof (int), 77 I've pasted the output below, and I've attached the config.log for reference.  I'm rea

[gmx-users] benzamide in top directory

Dear, all I find there are some small molecule's itp file in /gromacs/share/gromacs/top/; some of them seem belong to united atom force field, others of them seem belong to all-atom force field. Now, the question is, most of them has no note about which force field it belongs to, how can I know wh

Re: [gmx-users] force field

hjbai wrote: > Hi, all > What's the difference between different force fields? such as gromos 87, > gromos 96 and opls/aa, I was confused -- How can I get some information > about this? I have looked through the manual, and cant get a clear > picture for this problem. > Thank you, any kinds of disc

[gmx-users] force field

Hi, all What's the difference between different force fields? such as gromos 87, gromos 96 and opls/aa, I was confused -- How can I get some information about this? I have looked through the manual, and cant get a clear picture for this problem. Thank you, any kinds of discussion will be helpful.

Re: [gmx-users] MPICH or LAM/MPI

[EMAIL PROTECTED] wrote: Thank you very much you the advise, I will install fiors LAM and then MPICH. By the way you think can be interesting to invest in some low latenci network devices for this little clustter??. Or with the gigabit Can be enought Thanks Hector Of course the scaling wi

Re: [gmx-users] MPICH or LAM/MPI

Thank you very much you the advise, I will install fiors LAM and then MPICH. By the way you think can be interesting to invest in some low latenci network devices for this little clustter??. Or with the gigabit Can be enought Thanks Hector -Original Message- From: Carsten Kutzner <[

Re: [gmx-users] MPICH or LAM/MPI

Hello Hector, since it does not take long to install lam and mpich, I would install both MPI implementations and then benchmark with a typical MD system which one performs better. I would suggest LAM 7.1.2 which is the newest version, and MPICH-2 1.0.3, which works well, at least on our clus