Re: [gmx-users] force constants for umbrellla histograms

The most important is that you have to put in trajectories that are equilibrated! You can mix as much force constant values you like but always equilibrated ... Then the lower the force constant the longer the simulation needs to be to reach equilibrium: larger conformational space accessible. I

Re: [gmx-users] intersting problem

babu gokul wrote: dear all I want to calculate the how many water molecule are their with in 3.5 A of a particular atom. could anyone help me in this regard g_dist -dist -Justin E R Azhagiya singam -- Justin A. Lemkul Ph.D. Candidate ICTAS Doc

Re: [gmx-users] How to center molecules in the box with trjconj ?

ABEL Stephane 175950 wrote: Hi all, I have simulated a system containing 55 DPC molecules, a peptide some ions and water in a cubic box. Initially all molecules were placed randomly in the box. As expected during the simulation all the DPC molecules aggregate to form a stable micelle with the

Re: [gmx-users] force constants for umbrellla histograms

Thanks Xavier Then does it matter how many times you vary it, and how large ? In my sampling I have very good histograms up to 2 nm (force constant = 1000 kj/mol), above 2nm they are not. I feel I may have to use a force constant of 500 for the next 3 or 4 windows, and even less again (ca~ 50 kj/m

[gmx-users] intersting problem

dear all I want to calculate the how many water molecule are their with in 3.5 A of a particular atom. could anyone help me in this regard E R Azhagiya singam -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

[gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber

Ah! now I get it. Thanks Berk. On 20 August 2010 16:27, wrote: > Hi, > > That depends. > If you have explicit parameters in the dihedral section then 1 and 9 are > equivalent. > If grompp has to look up parameters in the dihderaltypes section there will > be difference > when multiple parameter

Re: [gmx-users] force constants for umbrellla histograms

On Aug 20, 2010, at 5:12 PM, Gavin Melaugh wrote: Hi all Is is O.K to use different force constants for different sampling windows for the generation of the potential of mean force curves? Yes. Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] How to center molecules in the box with trjconj ?

Hi all, I have simulated a system containing 55 DPC molecules, a peptide some ions and water in a cubic box. Initially all molecules were placed randomly in the box. As expected during the simulation all the DPC molecules aggregate to form a stable micelle with the peptide located at the micel

Re: [gmx-users] RE: Targeted MD

Hi, -r and -rb are for FEP. If you want to bias your simulation's sampling, you can use the pull code, essential dynamics sampling or flooding, all of which are described in the manual and literature. Ran Nimesh Jain wrote: > Hello, > > I realize that this topic has been discussed before, but I

[gmx-users] force constants for umbrellla histograms

Hi all Is is O.K to use different force constants for different sampling windows for the generation of the potential of mean force curves? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http:/

[gmx-users] RE: Targeted MD

Hello, I realize that this topic has been discussed before, but I just need to ascertain a few things: I have a system of about 1400 atoms with implicit solvent and I want to do a targeted MD. While doing the pre-processing, if I just specify "grompp -r in.gro -rb out.gro", is this sufficient or a

RE: [gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber

Hi, That depends. If you have explicit parameters in the dihedral section then 1 and 9 are equivalent. If grompp has to look up parameters in the dihderaltypes section there will be difference when multiple parameter lines are present the same atom types for a dihedral type 9. Berk From: ala

[gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber

Hi there, Now I have some results that I hope to clear this matter about dihe funct 4 and 9 (specially the latter). Please see: http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx >From my understanding (and results), where dihe funct 4 or 9, replacing both with 1 changes nothing in tot p

Re: [gmx-users] Trajectory protonation and inter proton distance calculation

It seems that my messages still are not getting through. I'll try again to post this today, apologies if you're getting multiple... Johannes Beck wrote: Dear Justin, dear all, thank you for your reply. Running protonate without defining an index file via -n is indeed possible, but when th

[gmx-users] sampled distances

Chris Again sorry for the delay. I posted a couple of times but the attachment was too big so I had to compress the file. Here is the histogram for the sampled distances. As you can see they are well behaved below 2nm, whereas above they are not. The histogram for the previous distance vs time p

[gmx-users] g_sorient

Dear all when i try to run g_sorient with g_sorient -f prod_full.xtc -s prod.tpr -o ANALYSIS/sorie nt/sori.xvg -no ANALYSIS/sorient/snor.xvg -ro ANALYSIS/sorient/sord.xvg I am getting a segmentation fault what would be the problem could anyone help in in this regard E R Azhagiya singam --

Re: [gmx-users] installation problem of gromacs binary

On 2010-08-20 09.14, Mark Abraham wrote: - Original Message - From: priyabrata panigrahi Date: Friday, August 20, 2010 16:56 Subject: [gmx-users] installation problem of gromacs binary To: gmx-users@gromacs.org > I was trying to install gromacs-3.3.3-1.x86_64.rpm. I got the following

Re: [gmx-users] installation problem of gromacs binary

- Original Message - From: priyabrata panigrahi Date: Friday, August 20, 2010 16:56 Subject: [gmx-users] installation problem of gromacs binary To: gmx-users@gromacs.org > I was trying to install gromacs-3.3.3-1.x86_64.rpm. I got the following error > > error: Failed dependencies: >