Re: [gmx-users] installing Gromacs with non-standard location of LAM/MPI

Hi, On Jun 7, 2006, at 6:53 AM, Mark Abraham wrote: Ivica Res wrote: Dear Mark, Thank you for the prompt answer. I did, however, compile FFTW with the --enable-float option, as I tried to explain in the original message. Ahh true. It is my understanding that this gives me the float

Re: [gmx-users] -translate option in editconf

Hi, On Jun 7, 2006, at 3:37 AM, Chris Gaughan wrote: I am trying to use the translate option in editconf to move my peptide ONLY in the x direction. thus I tried to use -translate 1,0,0. However, when I read the output from editconf it shows that it has translated my peptide 1,1,1. can anyone

[gmx-users] N/A

Hi, Can anyone suggest me is it possible to carry a minimisation followed by MD simulation in Groamcs in a water box keeping both the ligand and the substrate fixed?The backbone of the protein will also be fixed. regards SANGEETA KUNDU JUNIOR RESEARCH FELLOW BOSE INSTITUTE KOLKATA -- Open

[gmx-users] Freezing part of the molecules!!!

Hi all!!! I am trying to run a MD simulation with part of my system frozen. I was looking into the manual but I couldn't find the answer since the manual says the way for freezing complete groups. I would like to freeze only a part of my protein and permit the completed optimization of the rest.

[gmx-users] Trajectory sampling- NPT or NVT?

Title: Trajectory sampling- NPT or NVT? Hi all I am running diffusion simulation. When collecting my penetrant trajectories, shall I use NPT or NVT dynamics? It looks like references are divided about that... Thank you Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and

Re: [gmx-users] Freezing part of the molecules!!!

Hi!just make an index file (make_ndx) custom-defining the groups which you need to freeze, in your case the C-alpha of residues 18-42. Remember that, when you define new groups, you should delete the corresponding atoms from the group that contains all the rest of the protein atoms, if not you'll

[gmx-users] Free volume: Pass and Gromacs

Title: Free volume: Pass and Gromacs Hi all I wonder if anybody has been using Pass to measure free volume: I got these errors: -Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned. Suggestion: Do I have to remove all the dummies? -Segmentation fault Suggestion: I use

Re: [gmx-users] Free volume: Pass and Gromacs

Alessandro Mattozzi wrote: Hi all I wonder if anybody has been using Pass to measure free volume: I got these errors: -Error: Found an odd element (B) on atom #13454. Hydrogen radius assigned. Suggestion: Do I have to remove all the dummies? Yes. make an index file, it will have a

Re: [gmx-users] Freezing part of the molecules!!!

Hi Marcelo, what you need to do is: 1. create an index file (.ndx) with the groups that you want to freeze. Such an index file should look like: [ Group1 ] 45 46 47 48 49 ... [ Group2 ] 106 107 ... [ Group3 ] where atoms number 45, 46, 47, 48, and 49 etc

Re: [gmx-users] Freezing part of the molecules!!!

Soren Enemark wrote: Hi Marcelo, what you need to do is: 1. create an index file (.ndx) with the groups that you want to freeze. Such an index file should look like: [ Group1 ] 45 46 47 48 49 ... [ Group2 ] 106 107 ... [ Group3 ] where atoms number 45,

[gmx-users] shake vs settle for water

Hi All, I am using Groamcs 3.2.1 for my simulations, I am having some problems with an interfacial system when I use SETTLE as opposed to SHAKE to constrain OH bonds and HOH angle in water. As a matter of fact I did various simulations of liquid vapor interface simulations of water,

[gmx-users] diffusivity computations

Hi, I have trying to estimate the diffusivity of an alanine molecule in water with the following .mdp file (for md simualtions). ; Preprocessing title = Alanine with Water cpp = /lib/cpp include = define = ; Run Control integrator

Re: [gmx-users] shake vs settle for water

Rahul Godawat wrote: Hi All, I am using Groamcs 3.2.1 for my simulations, I am having some problems with an interfacial system when I use SETTLE as opposed to SHAKE to constrain OH bonds and HOH angle in water. As a matter of fact I did various simulations of liquid vapor interface

[gmx-users] Re: shake vs settle for water

Royal Institute of Technology Stockholm, Sweden -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060607/ace7fa15/att achment-0001.html -- Message: 2 Date: Wed, 07 Jun 2006 17:14:59

[gmx-users] persistence length

Hi, I was just wondering if it is possible to calculate the persistence length of a long chain-like molecule with one of the gromacs analysis programs or if anyone has anything else that will do this? Thanks in advance, -Syma *** Dr Syma Khalid

[gmx-users] Re: shake vs settle for water

/attachments/20060607/ace7fa15/att achment-0001.html -- Message: 2 Date: Wed, 07 Jun 2006 17:14:59 +0200 From: David van der Spoel [EMAIL PROTECTED] Subject: Re: [gmx-users] Free volume: Pass and Gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID

[gmx-users] AFM Pulling Rate

Hello everyone, I am using AFM pulling to drag a dna base across the surface of a graphene. I'm doing this in vaccuum. It seems that the base is pulled at the same rate no matter what value I specify in afm_rate1. Here is my pull.ppa file: runtype = afm group_1 = ssdna-ions pulldim = N N Y

Re: [gmx-users] Freezing part of the molecules!!!

Soren Enemark wrote: Quoting David van der Spoel [EMAIL PROTECTED]: Soren Enemark wrote: Hi Marcelo, what you need to do is: 1. create an index file (.ndx) with the groups that you want to freeze. Such an index file should look like: [ Group1 ] 45 46 47 48 49 ... [ Group2 ]

Re: [gmx-users] persistence length

syma wrote: Hi, I was just wondering if it is possible to calculate the persistence length of a long chain-like molecule with one of the gromacs analysis programs or if anyone has anything else that will do this? Plz give a definition (equation) Thanks in advance, -Syma

Re: [gmx-users] Re: shake vs settle for water

://www.gromacs.org/pipermail/gmx-users/attachments/20060607/ace7fa15/att achment-0001.html -- Message: 2 Date: Wed, 07 Jun 2006 17:14:59 +0200 From: David van der Spoel [EMAIL PROTECTED] Subject: Re: [gmx-users] Free volume: Pass and Gromacs To: Discussion list for GROMACS

Re: [gmx-users] drift of simulation cell

Qing Zhu wrote: Hi All, I am using gromacs to simulate a lipid/cholesterol mixed membrane. When I looked at the trajectory using VMD, the whole simulation cell laterally drifted very fast, and it looked like center of mass motion. But when I set up the simulation, I did turn off the center