Re: [gmx-users] Autocorrelation function comes to be zero

Den 2018-07-11 kl. 18:40, skrev SHYANTANI MAITI: Dear all, If the autocorrelation function is zero for a particular simulation, is there any problem in the simulation? Can autocorrelation come out to be zero for a simulation? What autocorrelation function? -- David van der Spoel, Ph.D., Profes

Re: [gmx-users] Making group of different atoms

Have you try make_ndx tool of Gromacs? On Wed, Jul 11, 2018, 00:09 Chetan Puri wrote: > Can someone guide me in how to make a group for atoms number 1566, 1567, > 1569,1571,1574&1579, which all belong to a tyrosine residue number 128 of > protein. > > Since I need to measure distance between two

[gmx-users] Autocorrelation function comes to be zero

Dear all, If the autocorrelation function is zero for a particular simulation, is there any problem in the simulation? Can autocorrelation come out to be zero for a simulation? -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.or

Re: [gmx-users] Flat bottom position restraints

Hi, The flat bottom potential acts in both directions out from the center you specify, so you should only need one potential - see figure 4.14 in the reference manual, panel A. Use a positive r value and positive force constant. Kevin On Wed, Jul 11, 2018 at 6:09 AM, Joe Wu wrote: > Yes I am!

Re: [gmx-users] Making group of different atoms

I think you can manually insert that into the index file (.ndx). On Tue, Jul 10, 2018 at 12:09 PM, Chetan Puri wrote: > Can someone guide me in how to make a group for atoms number 1566, 1567, > 1569,1571,1574&1579, which all belong to a tyrosine residue number 128 of > protein. > > Since I need

Re: [gmx-users] Help

https://www.urbandictionary.com/define.php?term=btw :) He wants you to try never version 2018.2: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018.2.tar.gz Also try different fftw options. On cmake line add: -DGMX_FFT_LIBRARY=xxx where xxx can be fftw, mkl or fftpack. You also need proper stuff inst

Re: [gmx-users] Help

Sorry, but... what is BTW 2018.2? Another software? El mié., 11 jul. 2018 a las 6:50, Mark Abraham () escribió: > Hi, > > I haven't seen that, and don't know how to guess what might make it work. > BTW 2018.2 is a better idea to install. > > Mark > > On Wed, Jul 11, 2018 at 3:34 AM Maximiliano Se

Re: [gmx-users] Flat bottom position restraints

Yes I am! On Wed, Jul 11, 2018 at 5:47 PM, Mark Abraham wrote: > Hi, > > Are you telling grompp to use your restraint.gro? > > Mark > > On Wed, Jul 11, 2018 at 9:43 AM Joe Wu wrote: > > > Hi Justin (or anyone else who can help), > > > > There was a post where Justin told us to look through the

Re: [gmx-users] (no subject)

Hi, Are you trying to observe something about the transition, or merely the different end points? Mark On Tue, Jul 10, 2018 at 4:12 PM Soham Sarkar wrote: > Dear all, > I am planning to do a simulation where after 50ns of simulation I want to > add some other chemicals in the system and conti

Re: [gmx-users] Help

Hi, I haven't seen that, and don't know how to guess what might make it work. BTW 2018.2 is a better idea to install. Mark On Wed, Jul 11, 2018 at 3:34 AM Maximiliano Sebastián Castillo < mcasti...@itba.edu.ar> wrote: > Hello, > I have the next problem: > [ 1%] No patch step for 'fftwBuild' >

Re: [gmx-users] Flat bottom position restraints

Hi, Are you telling grompp to use your restraint.gro? Mark On Wed, Jul 11, 2018 at 9:43 AM Joe Wu wrote: > Hi Justin (or anyone else who can help), > > There was a post where Justin told us to look through the archive for > detailed steps as to how to set up flat bottom restraints, but I canno

Re: [gmx-users] topolgen

Try running this command from the directory where topolgen.pl script is present. On 11/07/2018 09:43, farial tavakoli wrote: Dear gromacs users I am trying to run a simulation on my complex which has small molecule as a ligand , using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then in

[gmx-users] topolgen

Dear gromacs users I am trying to run a simulation on my complex which has small molecule as a ligand , using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then installed perl script on linux. then typed "perl -v" to check if it is installed. the perl 5.20.1 is installed. but when I typed

[gmx-users] Flat bottom position restraints

Hi Justin (or anyone else who can help), There was a post where Justin told us to look through the archive for detailed steps as to how to set up flat bottom restraints, but I cannot find it. I've been looking through the entire archive for that post where he explains in detail. Can anyone help ou

[gmx-users] mpirun and gmx_mpi

Hi,Although I have read the manual and I have wrote programs with mpi, the gromacs use of mpi is confusing. Is it mandatory to use mpirun before gmx_mpi or not? Can someone shed a light on that? Regards, Mahmood -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.or