Re: [gmx-users] gpu k20x vs k40

On 20.05.2014 08:13, Andrei Neamtu wrote: We are currently in the process of buying several servers which will include GPU accelerato. Because of the price / performance balance in case of our limited funds we have to choose between K40 and K20X tesla accelerators. Initially, we wanted 2 GPU's/no

Re: [gmx-users] gpu k20x vs k40

Dear Mirco, Many thanks for your reply! It is a server rack based solution. Mainly plain molecular dynamics with PME. Thanks, Andrei *Dr. Andrei Neamtu, PhD, Lecturer Department of Physiology "Gr. T. Popa" University of Medicine and Pharmacy of Iasi http://www.umfiasi.ro/

[gmx-users] entropy vs time plot

Dear All, Could anyone tell me how to plot configurational entropy as a function of simulation time? Do I need to manually specify the -dt(say after each 1 ns) during the g_covar and then do g_anaeig in each of the step? thanks, Tarak -- Gromacs Users mailing list * Please search the archive at

[gmx-users] High density after genbox

Hello, I am working on a water-methane system with OPLSAA for methane and TIP4P/Ice for water. What I find strange is that after solvating the methane molecule with water (tip4p/ice) using the genbox routine, the density appears to be very high at 1661.04 (g/l) . The number of water molecules

[gmx-users] Reference value for berger POPC area per headgroup

Hi I have a question about which value to aim for as a reference for the berger lipids and POPC area per head group. In Justin Lemkul's tutorial, the value 65.8 A^2 is reported, along with a reference to a 1998 Tieleman et al. paper. However, I have read that paper now twice and cannot find this

[gmx-users] how to select heavy atoms of Ligand

Dear all, I would like to make index file of heavy atoms of ligand by g_select command. However, I don't know how to select heavy atoms of ligand. I tried g_select -select "resname LIG and not name H" command, but it did not work. Could you tell me any advice? Bests, Atsutoshi Okabe -- Gromacs

Re: [gmx-users] how to select heavy atoms of Ligand

Dear Atsutoshi, first you could make a new group by means of make_ndx: make_ndx -f foo.gro (you complex) -o index_new.ndx here when asked you should type: group numer of your ligand & !a H* For other analysis call the index already done with -n index_new.ndx Cheers Josephine __

Re: [gmx-users] Reference value for berger POPC area per headgroup

Hi, You can have a look at: http://pubs.acs.org/doi/abs/10.1021/ct3003157 In these simulations I used a few different variants in terms of both cut-off's and the 'Berger' force field parameters, and so there isn't just one reference value as the APL is dependent upon these different parameters

Re: [gmx-users] Combining .edr-files with eneconv

Hi, That all seems very strange. It looks like you're running MPI-enabled tools, and from your build tree rather than an install tree. Neither of those uses are encouraged (almost no tools support MPI), though they may work. I would do a proper install, and configure without MPI, to remove various

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

Dear Justin, Thank you for your email. As in your case, my system is formed by a Protein + dsDNA + structural ions + counterions + ligand + water I guess that I have too much element to efficiently solve the problem but I want to try to fix it. The solution could help other people to avoid to be

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

On 5/20/14, 1:14 PM, Vito Genna wrote: Dear Justin, Thank you for your email. As in your case, my system is formed by a Protein + dsDNA + structural ions + counterions + ligand + water I guess that I have too much element to efficiently solve the problem but I want to try to fix it. The solu

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

Hi Vito, Was the structure already broken up when you solvated it? If not, which seems likely to me, then you can use that structure, or the .tpr from the EM in solvent, to remove jumps from the first frame of your run. After you unbroke the first frame, you can use that as reference for processin

Re: [gmx-users] entropy vs time plot

Hi Tarak, You will have to use -b/-e to set the start and end times. Cheers, Tsjerk On Tue, May 20, 2014 at 12:18 PM, tarak karmakar wrote: > Dear All, > Could anyone tell me how to plot configurational entropy as a function of > simulation time? > Do I need to manually specify the -dt(say af

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

Hi Tsjerk, Thank you for your email. No it is not broken. The structure is intact till the 20 ns of production phase. I have already used the .tpr (both md_0_1.tpr before, and then npt.tpr) obtaining the same result. Basically you are suggesting to fix the first frame of the production phase and

Re: [gmx-users] High density after genbox

Probably "garbage in, garbage out." However you're measuring the density probably depends on share/top/atommass.dat, which relies on matching atom names to infer atom types and thus masses. If your atom names don't follow its assumptions... at least some tools warn about this in the output. Did the

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

Hi Vito, If the .tpr file is good, i.e. has everything assembled the way you want, then the first step is trjconv -pbc nojump. That will make sure that nothing gets split over PBC. Then center the protein in the box (trjconv -center), and subsequently put all molecules in the box (-pbc mol -ur com

[gmx-users] Need guidance

Hi Everyone, Need guidance and help. As I am doing md simulation for Lysozyme in presence of gold i.e Au(111) with force field oplsaa and Golp parameters . What I am doing is first generating .top file for protein with oplsaa force field and then using Golp gold .itp and .gro file parameters a

Re: [gmx-users] entropy vs time plot

Hi Tsjerk, Thanks for the quick reply. I did the following g_covar -f ../../npt_prod -s ../../npt_prod -n loop_II.ndx -o eigenval -v eigenvec.trr -av average.pdb -b 0 -e 1 g_anaeig -v eigenvec -entropy -temp 300 -b 0 -e 1 What I want to plot is similar to this. http://www.ncbi.nlm.nih.gov