[gmx-users] Re: GPU-based workstation

I have nothing to contribute regarding the CPUs, but note that last week Nvidia introduced the GTX 780 GPU (a Titan lite), and this week it is expected to introduce the GTX 770 one (probably an overclocked 680). Therefore, disregarding possible price issues, it seems that the GTX 680 may not be

Re: [gmx-users] GPU

the development team would reconsider GPU accelerating also minimizations. I suspect this would not be technically too complex given the work already done on dynamics. Thanks, Ehud Schreiber. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] a request regarding pdb2gmx and specbond.dat

. These two values would be optional, so as not to break the existing arrangement, which would remain as the default. This should not require more than a few extra lines of code and would be, in my opinion, very useful. What do you say? Thanks, Ehud Schreiber. -- gmx-users mailing list

[gmx-users] trjconv -dump problem

why the expected timeframe isn't reproduced? I'm using gromacs 4.5.3. Thanks, Ehud Schreiber. -- 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

[gmx-users] FW: trjconv -dump problem

217.000 . . Also, using -dump 200 gave an identical file to the above. Any idea why the expected timeframe isn't reproduced? I'm using gromacs 4.5.3. Thanks, Ehud Schreiber. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] RE: trjconv -dump problem

did not produce a checkpoint file (I'm not sure whether because I didn't ask to or because the run was shorter than 15 minutes). Thanks, Ehud Schreiber. -- Message: 2 Date: Tue, 14 Feb 2012 21:58:10 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re

[gmx-users] N-Acetylglucosamine (NAG) in OPLS-AA

; copied from opls_140 ; opls_229 0.18 1 1.2760.1900.72 ; copied from opls_158 ; So, are my choices reasonable? Could this have been done in some easier fashion? Thanks, Ehud Schreiber. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] RE: How to obtain structures with large RMSD?

Hi, You can try the non-gromacs tool Concoord: http://www.mpibpc.mpg.de/groups/de_groot/concoord/ http://151.100.52.62/pdf/046_amadei_proteins_1997.pdf It was used e.g. in the CC/PBSA algorithm http://ccpbsa.biologie.uni-erlangen.de/ccpbsa/

RE: Re: [gmx-users] opls-aa, implicit solvent and GPUs

-1252; format=flowed Ehud Schreiber wrote: Hi, I'm currently utilizing gromacs using the opls-aa forcefield in an implicit-solvent setting. Can any of the developers roughly predict in what version, and when, will GPU acceleration be applicable for such work? I am afraid

[gmx-users] opls-aa, implicit solvent and GPUs

Hi, I'm currently utilizing gromacs using the opls-aa forcefield in an implicit-solvent setting. Can any of the developers roughly predict in what version, and when, will GPU acceleration be applicable for such work? I am afraid the gromacs 4.6 roadmap webpage left me confused. By the way,

[gmx-users] pdb2gmx, disulfide bonds and PDB CONECT lines

a topology with the desired disulfide bonds? Preferably the solution should be non-interactive as I handle multiple perturbed structures. The perturbations use an existing utility so must be performed on the PDB level. Thanks, Ehud Schreiber. -- gmx-users mailing listgmx-users

[gmx-users] pdb2gmx with input topology

Dear Gromacs users, I wish to convert PDB files to gromacs format while specifying the topology; however, in the pdb2gmx program, a .top file can only be an output, not an input. The need arises as I have an NMR PDB structure (including hydrogens) which I rather violently perturb into

[gmx-users] RE: g_energy inconsistent results

...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 8/03/2011 9:44 PM, Ehud Schreiber wrote: Dear Gromacs users, I am working with version 4.5.3, using the opls-aa forcefield in an implicit solvent, all-vs-all setting: pdb2gmx -ter -ff oplsaa -water none -f file.pdb I am energy

[gmx-users] g_energy inconsistent results

Dear Gromacs users, I am working with version 4.5.3, using the opls-aa forcefield in an implicit solvent, all-vs-all setting: pdb2gmx -ter -ff oplsaa -water none -f file.pdb I am energy-minimizing structures in 3 stages (steep, cg and l-bfgs). The last stage is the following:

[gmx-users] Simulated Annealing parameters

mentioned above. Am I doing anything wrong? If not, the correct behavior would be to warn when this parameter is specified rather than to demand it (and then presumably ignore it). Thanks in advance for your thoughts on the matter, Ehud Schreiber. -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Generalized Born in GROMACS manual

Dear GROMACS users, I have looked into some of the literature in order to understand better implicit solvent models, in particular the generalized Born formalism. I believe that section 3.18 of the v4.5 GROMACS manual, dealing with the above, is in need of some corrections: 1) In eq.

[gmx-users] RE: Gibbs free energy of binding

...@xray.bmc.uu.sewrote: On 2010-10-21 10.39, Ehud Schreiber wrote: Actually, I believe that using the energy difference, Delta E, as an approximation to the free energy difference, Delta G, is a valid approach (which I'm considering myself). The entropic contribution to Delta G, namely -T Delta S, may

[gmx-users] RE: Gibbs free energy of binding

Actually, I believe that using the energy difference, Delta E, as an approximation to the free energy difference, Delta G, is a valid approach (which I'm considering myself). The entropic contribution to Delta G, namely -T Delta S, may be less prominent than Delta E. In addition, Delta S can be

[gmx-users] RE: Energy Minimization

Hi, I would allow flexible water by uncommenting the line define = -DFLEXIBLE and trying again; reducing the time step might also be required. Message: 4 Date: Mon, 18 Oct 2010 16:26:16 -0400 From: Sai Pooja

[gmx-users] best parameters for energy determination with GBSA

Dear GROMACS users, I try to compute energies of a small peptide-domain complex and of its constituents using implicit solvent, so that I can get the binding Delta E. I need the accuracy to be high enough so that I can reliably measure the Delta Delta E between the wildtype peptide and a

[gmx-users] potential energy in implicit solvent simulations

Dear GROMACS users, I am conducting energy minimization with an implicit solvent, using GROMACS version 4.5.1 at double precision. The minimization provides the minimal potential energy I'm interested in, but I also wanted to see the contributions to it. I therefore used g_energy_d and

[gmx-users] grompp_d and mdrun_d issues with GBSA and normal mode analysis

[file nm.mdp]: With GBSA, coulombtype must be equal to Cut-off Am I doing something wrong or are there still some problems in the new GBSA option of version 4.5.1? Thanks, Ehud Schreiber. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

[gmx-users] RE: [nonbond_params] section , choice of parameters

Hi Amir, Are you sure you're giving the parameters indeed as C_6 and C_{12}? According to the combination rule in the [ defaults ] section, you may be giving the two parameters directly as sigma and epsilon; sigma=0 (as well as epsilon=0) would give an identically zero potential . See

[gmx-users] RE: RE: [nonbond_params] section , choice of parameters

changed to the combination rule=1 convention. From: Ehud Schreiber Sent: Wednesday, July 28, 2010 3:01 PM To: 'gmx-users@gromacs.org' Subject: RE: [nonbond_params] section , choice of parameters Hi Amir, Are you sure you're giving the parameters indeed as C_6 and C_{12}? According

[gmx-users] HA1/HA2 chirality of GLY

is it? As most PDB files do not contain hydrogens, this question seems to be about the behavior of pdb2gmx when creating a .gro file with an all-atom force field (such as opls-aa). Thanks, Ehud Schreiber. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] large forces and monstrous water molecules in energy minimization step

integrator = cg, is even worse - the running crashes: ... Step 16, Epot=-1.258771e+35, Fnorm= nan, Fmax= inf (atom 14493) Segmentation fault Exit 139 So, am I doing something wrong? How can I avoid these problems? Thanks, Ehud Schreiber. -- gmx-users mailing listgmx