[gmx-users] mixing of PCs for generating reduced free energy profile using g_sham

Hi Gromacs user community a) I was wondering if it is possible to mix a common pair of PCs from two simulations (say, PC1 from a bound simulation vs PC1 from unbound simulation or for that matter wild vs mutant) as an reaction coordinates to generate a comparative reduced free energy profile

Re: [gmx-users] Re: Attention:urgent

Plz be very specific about your problem. In fact iam not able to find out that problem is. what is the error msg what did you do do you need a sge script to submit job in a super computer or a cluster??? if so then what queing system all thes ethings are very imp On Thu, Jul 26, 2012 at 7:33 AM,

[gmx-users] RIMSP calculation

Hi Gromacs users I am trying to measure the similarity of the subspace sampled by a mutant protein-Ligand complex versus a wild type complex based on the eigen vectors computed using PCA. I was wondering, does and handy scripts does exists to compute the root mean square inner product (

Re: [gmx-users] RIMSP calculation

Hi Tsjerk Many thanks for your kind response. Got the script, will try to run it. Also thanks for clarifying RMSIP vs Cosine content values. Regards Vijayan.R On Thu, Jun 28, 2012 at 10:56 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Vijayan, There must be a script somewhere in the

Re: [gmx-users] constraints between protein ligand - metal chelation

Francesco 2012/5/20 R.S.K.Vijayan biovija...@gmail.com Many thanks for your response. No special reasons for parametrizing the ligand and the protein as a separate system. I dont think that the ligand and protein can be parametrized as a single system, but will definitely try doing

[gmx-users] constraints between protein ligand - metal chelation

Dear Gromacs users I was wondering if there exists any technique that sets distance restraint between specified ligand (atoms) and the protein(atoms) in Gromacs. I am simulating a system which contains metal ions coordinated to the Ligand. I looked in to the mailing list and Gromacs manual and

Re: [gmx-users] constraints between protein ligand - metal chelation

moleculetype and use distance restraints there, can't you? On 2012-05-19 09:42:25PM -0400, R.S.K.Vijayan wrote: Dear Gromacs users I was wondering if there exists any technique that sets distance restraint between specified ligand (atoms) and the protein(atoms) in Gromacs. I am

[gmx-users] query about identifying representative snapshots from a 2D FEL

Dear Gromacs users I am interested in identifying the representative snapshots from a 2D Free energy landscape plot generated using g_sham using the reaction coordinates obtained from EV1 and EV2 projections. Can some suggest on how to back trace the coordinates from a 2D FEL and also the

[gmx-users] Simulating multiple fragments

Hi all I was wondering if some body has done simulating multiple copies of small lead like fragments in a solvated box . I want to soak my proteins with multiple copies of diverse fragments along with water as iam interested in finding the hot spots in proteins that can be successfully

Re: [gmx-users] discrepancy between ED motions and the MD motion

. As a sidenote, do check whether it is a biologically relevant motion, or merely relaxation. Cheers, Tsjerk On Dec 21, 2011 4:24 PM, R.S.K.Vijayan biovija...@gmail.com wrote: Hi all I carried out a distance analysis between two domains with respect to time based on the center of mass

[gmx-users] Eigenvalue values from PCA (a general question)

Hi all I have a query about the eigenvalue values obtained from g_covar and g_anaeig I performed essential dynamics using PCA on my system (Protein-DNA complex) considering BB of the protein and the phosphate and sugar of the DNA for a 50 ns trajectory. The eigenvalue which i do obtain for the

Re: [gmx-users] Eigenvalue values from PCA (a general question)

Hi Tsjerk Many thanks for your response. Do you think NMA is worth considering in such cases like this? Regards Vijayan.R On Thu, Dec 15, 2011 at 3:39 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Vijayan R., What i infer from this is that the cumulative variance experienced by the

Re: [gmx-users] Eigenvalue values from PCA (a general question)

Thanks Tsjerk On Thu, Dec 15, 2011 at 4:55 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Vijayan.R, Not really. NMA also assumes linear relationships. Cheers, Tsjerk On Thu, Dec 15, 2011 at 10:48 PM, R.S.K.Vijayan biovija...@gmail.com wrote: Hi Tsjerk Many thanks for your

Re: [gmx-users] Re: Eigenvalue values from PCA (a general question)

Thanks Micheal for pointing out the mistake On Fri, Dec 16, 2011 at 4:20 AM, Niesen, Michiel mnie...@coh.org wrote: Date: Thu, 15 Dec 2011 15:11:12 -0500 From: R.S.K.Vijayan biovija...@gmail.com Subject: [gmx-users] Eigenvalue values from PCA (a general question) To: gmx-users@gromacs.org

[gmx-users] Cosine content

Dear Gromacs users I have a question regarding cosine content. I have a 50 ns trajectory and looking at the RMSD plot, i set aside the first 5 ns as the time required for stabilization and subsequently carried out a essential dynamics for the backbone atoms post 5ns. But when i perform a

[gmx-users] MM/PBSA Gromacs

Dear Gromacs users Is there any script that does a PB or GB calculation to perform a MM/PB(GB)SA free energy calculation in Gromacs. Similar to the MMPBSA.py script available in Amber. I find a similar question raised by a user a couple of years back. Any successful implementation

[gmx-users] SASA query

+ligand)** is this the right procedure. R.S.K.Vijayan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests