Re: [gmx-users] How to set the temperatures for REMD?

Hi, On Wed, Jan 22, 2020 at 5:55 PM ZHANG Cheng <272699...@qq.com> wrote: > My purpose of running REMD is to generate sufficient conformation > sampling, and try to use them to explain the in vitro data at 65C (338.15K). > > > I am using the "Temperature generator for REMD-simulations" at > http

Re: [gmx-users] Problem of lincs in free energy calculations

Usually, in this case, Lincs algorithm is not the cause of unstable MD simulation. It is symptome of possible blowing up. Possible reasons are described here http://www.gromacs.org/Documentation/Terminology/Blowing_Up Alex ср, 22 янв. 2020 г. в 12:57, Sadaf Rani : > Dear Gromacs users > During fr

Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize

I tried just now: it did not work: 1728 values expected, 1645 values in the .dat file. I managed to make it work by defining the number of values in each direction as (in Python): Nx = np.sqrt(Nda*Lx/Lz) Nz = Nx*Lz/Lx Nx = int( np.round(Nx) ) Nz = int( np.round(Nz) ) being Nda the number of value

Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize

I will try, thank you for the tip. To be fair, this issue came up also when trying to set a meshwidth larger than the one GROMACS prescribes by default (I was trying 0.05 nm instead of 0.02 nm). Cheers, Michele From: gromacs.org_gmx-users-boun...@maillist.

Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize

Den 2020-01-22 kl. 18:44, skrev Michele Pellegrino: Ok, thank you. I am counting the elements assuming they are in an array organized in a row major fashion. have you tried supplying -n1 47 -n2 35 to be able to check manually? (by the way a resolution of 0.1 Angstrom is unlikely to give you a

Re: [gmx-users] .dat file from gmx densmap doestnottmatchtprescribedtsize

Ok, thank you. I am counting the elements assuming they are in an array organized in a row major fashion. Scarica Outlook per Android From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Berk Hess Sent: Wednesday, January

[gmx-users] How to run REMD for EM, NVT, NPT and production run?

I have gone through Mark Abraham's tutorial on REMD http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B Now I would like to run my own REMD, adjusted from Justin's Lysozyme tutorial

Re: [gmx-users] .dat file from gmx densmap does not match prescribed size

A grid element I looked at the code and it directly uses n1 and n2 you provide. So I thought that it might be that the code reading the file has a limit on the number of characters on a line. /Berk From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on be

[gmx-users] How to set the temperatures for REMD?

My purpose of running REMD is to generate sufficient conformation sampling, and try to use them to explain the in vitro data at 65C (338.15K). I am using the "Temperature generator for REMD-simulations" at http://folding.bmc.uu.se/remd/ I am not sure about the "standard/default" values of sev

Re: [gmx-users] .dat file from gmx densmap does not match prescribed size

What do you mean by 'element'? Anyway, part of the issue was in how I was reading the file; with a little modification of the script I reduced the mismatch, but it still persists. Could it be because GROMACS forces a grid with same meshwith in x and (in my case) z direction, so that the used s

Re: [gmx-users] .dat file from gmx densmap does not match prescribed size

How are you counting the elements? Lines with 3531 elements are very long, so they can easily exceed some limit. /Berk From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Michele Pellegrino Sent: Tuesday, January 21, 2020 5:16 PM To: gromacs.

[gmx-users] Fourier dihedrals

Dear all, I am looking in the manual at how the Fourier dihedrals are defined, and there appears to be a discrepancy between section 5.5 and the table of topology directives in 5.14. 5.5 shows an equation with four coefficients (F1, F2, F3, F4), whereas the table shows 5 coefficients for the Fo

[gmx-users] Problem of lincs in free energy calculations

Dear Gromacs users During free energy calculation, I am getting lincs warning at MD run in some of Lambda windows. To cope with this I have reduced my time step to 1 fs rather than 2. Some of them converged but for others, it still gives lincs warning and generates different PDB structures. If the

Re: [gmx-users] top2psf license

I have contacted the author Marc Baaden and he has told me that the script should be distributed under BDS-3 clause version. Please if you do modify or distribute this script make sure you copy the license text in the header. He's also asked me to share that unity Mol can determine topology and se

Re: [gmx-users] Assertion failed for the REMD tutorial

Hi, On Tue, Jan 21, 2020 at 9:55 PM ZHANG Cheng <272699...@qq.com> wrote: > I am trying to follow the REMD from Mark Abraham at > > http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B

[gmx-users] top2psf license

Does anyone know what the license is for the top2psf.pl script. I'd like to modify and distribute it if possible. Best, Miro. -- 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.