[gmx-users] Optimum slice size (-sl)

Hello GROMACS users, What is the optimum slice size when trying to capture as much variation as possible? Consider a box with an electrolyte having anions and cations distributed in it. *Would be accurate to specify a slice size smaller than the diameter of the ions while calculating the

Re: [gmx-users] Installation problem

Hi, The system has a gpu (gtx 590) with cuda libraries installed (I've run namd on the system). It also has mpi: mpic++ mpiCCmpiCC.openmpimpicxx mpiexec mpif77 mpif90 mpirun mpiccmpicc.openmpimpic++.openmpi

[gmx-users] pulling simulation

Dear all, I'm trying to do umbrella sampling. But after running "perl distances.pl", I get a "summary_distances.dat file which has NO distances! Before, I get an error "pull reference distance for group 1 is negative" while I run grompp and then mdrun for pulling simulation. Below is my

Re: [gmx-users] Optimum slice size (-sl)

the ions may have a radius, but they are distributed continuously along the system, so you may use slice thicknesses smaller than the ionic radius you're interested in. if the simulation was made on some sort of lattice system (which was very common back in the 1990's), then the shortest,

Re: [gmx-users] Installation problem

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

Re: [gmx-users] DSSP secondary structure

On 2/13/16 1:33 AM, mohammad r wrote: Hi, I used the "gmx do_dssp" command to get the secondary structure of the protein during the simulation but the resolution of the resulted .xpm file is very low. how can I increase its resolution? You can adjust the matrix proportions with an .m2p

Re: [gmx-users] pulling simulation

On 2/13/16 10:24 AM, Mehrnoosh Hazrati wrote: Dear all, I'm trying to do umbrella sampling. But after running "perl distances.pl", I get a "summary_distances.dat file which has NO distances! Before, I get an error "pull reference distance for group 1 is negative" while I run grompp and then

Re: [gmx-users] Optimum slice size (-sl)

If you are using a slice and PME, then wouldn’t the slice have to be thick enough to avoid any ion interacting with its own image in adjacent slices? It seems to me that thickness would have to be greater than the ionic radius at the very least. Warren Gallin > On Feb 13, 2016, at 8:39 AM,

Re: [gmx-users] Prodrg disturbed hybridization state of doubly bonded nitrogen

On 13/02/16 08:11, Saman Yousuf ali wrote: Dear all,I am a beginner here. I have prepared my ligand topology file using prodrg, it gave me the following error, PRODRG> Starting up PRODRG version AA100323.0717PRODRG> Parameter set 'pd/gromos96' (fftype=2).PRODRG> PDB mode detected.PRODRG>

Re: [gmx-users] Optimum slice size (-sl)

50 slices corresponds to a slice size slightly smaller than the smallest ions' diameter. On Sat, Feb 13, 2016 at 4:40 PM, Ashutosh Akshay Shah wrote: > Thank you Andre and Warren! > > A note about PME- > The basic principle is that a system of particles is converted into

[gmx-users] energygrps

Dear Gromacs user, By using "energygrps = A SOL" We can have SR-NB potential energies between "SOL"-"A" in the energy file, now suppose that there are three elements with different population in our system like "A", "B" and "SOL", my question is that what should I write as "energygrps" if the

Re: [gmx-users] Optimum slice size (-sl)

Thank you Andre and Warren! A note about PME- The basic principle is that a system of particles is converted into a grid (or "mesh") of density values. The potential is then solved for this density grid, and forces are applied to each particle based on what cell it is in, and where in the cell it

Re: [gmx-users] energygrps

On 2/13/16 5:43 PM, Alexander Alexander wrote: Dear Gromacs user, By using "energygrps = A SOL" We can have SR-NB potential energies between "SOL"-"A" in the energy file, now suppose that there are three elements with different population in our system like "A", "B" and "SOL", my question is

[gmx-users] Simulation Terminated on Clusters Due to "cannot rename checkpoint file"

D​ear gmx users, Just a little revision for my last question. I am running my cases on the cluster. The simulation was always terminated after running for a while. The error was always " *cannot rename checkpoint file: maybe you are out of disk space*". However, I have 1TB of disk allocation,

Re: [gmx-users] DSSP secondary structure

Thank you Justin, I used xpm2ps command with below m2p file but the resolution was not changed. I've attached the xpm file, even the legend can't be seen.is there anyway to get the result file in pdf format? m2p file (I found it in the gromacs website): black = no ; Obsoletetitlefont =