[gmx-users] BCAM Internship Position Announcement

BCAM Internship Position Announcement The following BCAM Internship position is open at BCAM – Basque Center for Applied Mathematics, an interdisciplinary research center located in Bilbao. The interested applicants can apply via the following webpage: http://www.bcamath.org/en/research/interns

Re: [gmx-users] Problems with g_anaeig

Mark, By 'coverage' I mean the 1 value in the dot product of the comparing eigenvectors sets (between 1 and 1, 2 and 2 and so on eigenvectors) ( that indicate that both eigenvector set are identical as I suppose). In that case I had 2 identical pdp ensembles from which in 1 case I obtained normal

RE: [gmx-users] Re: On the choosing of GPU for MD runs

Hi, Performance in single precision on Tesla cards is often lower than on GTX cards. The only reason to buy Telsa cards is double precision, reliability and fanless cards for clusters. I have a GTX 660 Ti, which is much cheaper than a GTX 670, but should have nearly the same performance in Gro

Re: [gmx-users] Hydrogen bonding differences

Dear Sir, Sure I will try with 4.6. presently I am not able to download it. Thank you kavya On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund wrote: > There were a handful of bugfixes to g_hbond over the last year. Could you > try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form befo

Re: [gmx-users] Hydrogen bonding differences

There were a handful of bugfixes to g_hbond over the last year. Could you try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form before. Erik On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote: Dear Sir, This is 4.5.3. I have not tried nomerge. I did not use nomerge option in any

[gmx-users] Distance matrix of the trajectory

Dear users, While calculating the distance matrix using g_mdmat, with -no option, it gives an xvg output pertaining the total, mean etc contacts of the residue within 1.5Ang in the trajectory. I calculated the same for a single frame (or pdb file) #resratio tot mean natm mean/atm 1

Re: [gmx-users] Charge on the protein

You're modelling a real physical system. You've chosen some ionization states, perhaps implicitly. Do those make sense for what you are modelling? Does a charged system make sense for what you are modelling? Mark On Fri, Jan 25, 2013 at 10:07 AM, wrote: > Hello > > while executing grompp follow

Re: [gmx-users] Problems with g_anaeig

On Fri, Jan 25, 2013 at 6:40 AM, James Starlight wrote: > Mark, > > as I told previously to Justin ( lets to consider the problems with > g_anaeig only in that topic to avoid producing doubles ) the problem > is not in the average structure (it looks fine) You might have noticed I made no mentio

[gmx-users] Charge on the protein

Hello while executing grompp following message is seen although the .tpr file is generated System has non-zero total charge: -3.00 Total charge should normally be an integer I have used AMBER99SB as the force field to prep the topology to run implicit solvent simulation. How relevant

[gmx-users] Re: aligning problem (hao)

> -- > > Message: 4 > Date: Fri, 25 Jan 2013 14:17:31 +0800 > From: Terry > Subject: Re: [gmx-users] aligning problem > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset=UTF-8 > > Check this: http://manual.gromacs.org/o

Re: [gmx-users] RMSD

On Jan 25, 2013, at 5:53 AM, Shima Arasteh wrote: Thanks for your reply. I want to chose one of the 5 conformers from a NMR PDB. As I studied in literature, the average structure could be selected regarding RMSD values and the go on with selected one to simulate in in water, lipid bilay

RE: [gmx-users] switching and shifting in GMX 4.6 on GPUs

Hi, The nomenclature is confusing here. I don't recall the details of the switching in CHARMM. But switch in Gromacs refers to switching the potential. Shift in Gromacs refers to switching the force and thereby shifting the potential. A switch on the force only (thus "shift" in Gromacs) can usu