Re: [gmx-users] Force field for urea and urea-TMAO mixture

Hi, The urea model of Lorna Smith ( https://pubs.acs.org/doi/abs/10.1021/jp030534x ) should be compatible with GROMOS force field. Best regards Alessandra On Wed, Mar 4, 2020 at 7:00 AM ISHRAT JAHAN wrote: > Dear all, > I want to do MD simulation of protein in urea and urea-TMAO mixture. Can >

Re: [gmx-users] Amber14SB

Hi, Here a page of force field in GROMACS http://manual.gromacs.org/documentation/current/user-guide/force-fields.htm maybe it helps. I did not fully understand your question Best regards Alessandra On Tue, Mar 3, 2020 at 10:04 AM Eduardo Mayo wrote: > Hi!! > I'm sorry if is the amber14sb post

Re: [gmx-users] Regarding REMD using gromacs4.5.5

Thank You Daniel Burns, Actually, right now I am looking at the installation and trying to install fresh as I found some error and created mess again while rectifying each one. At the time of installation "mdrun_mpi -h" worked perfectly so I thought installation is fine. But really thank you for yo

Re: [gmx-users] PEG from ATB: No residues in chain

Yes, there is no protein/DNA/RNA in my system. Do I have to define this somewhere? I get the warning when executing pdb2gmx. -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se Im Auftrag von Alessandra Villa Gesendet: Mittwoch, 4. März 2020 17:26 An: gmx-u

[gmx-users] Odd temperature spikes during T-REMD?

Good morning, I am experiencing a very bizarre problem during my T-REMD simulations of a (single-glycosylated residue) protein in water. During my T-REMD simulations, I find that my temperatures jumps from the expected range (my replicas are spaces between 310 to 350K) to 1000K or higher for 10

Re: [gmx-users] GMX 2020 - COMM Removal Issue

I agree, but this was a very short simulation (1 ns), so the size of the drift (several nm) was unexpected. To test, I repeated the simulation with GROMACS 2019.6 using all the same settings (but without the new ones: GMX_GPU_DD_COMMS, GMX_GPU_PME_PP_COMMS, GMX_FORCE_UPDATE_DEFAULT_GPU), and I don'

[gmx-users] how to add c-terminal to the coarse-grained structure

Hi, I am trying to convert all-atom system to coarse grained system using martini. I am encountering a problem with the C terminal of the protein. *Atom OT1 in residue LYS 45 was not found in rtp entry LYS with 22 atomswhile sorting atoms.* This is because Lysine 45 is at the end of C-terminal

Re: [gmx-users] PEG from ATB: No residues in chain

Hi, Why do you need to execute gmx pdb2gmx if you already retrieved parameters from ATB? ATB should be able to provide you the coordinate and topology files (.gro and .itp respectively) compatible with GROMACS. Soumadwip -- Gromacs Users mailing list * Please search the archive at http://www.gr

[gmx-users] gmx hbond -life

Dear Gromacs users I am analyzing the hbond lifetime between two residues by using gmx hbond -life. I attached the result xvg file and would like to know the explanation of the second column. I made different ndx file to check it but found both the sum of the second column is 0.01. Could you give

[gmx-users] core dump

Hello everybody I have been using GROMACS 2018.1 in the last month and I got an error "core dumped" while running the simulation. Accordingly, I have installed the 2020.1 version and while I am doing pressure equilibration (npt), I had the same error again (I paste it below) which is core dumped.

Re: [gmx-users] core dump

http://www.gromacs.org/Documentation/Errors#Pressure_scaling_more_than_1.25 System is unstable, there is a problem with with your topology or coordinates. On Fri, 6 Mar. 2020, 6:53 am Mohamed Abdelaal, wrote: > Hello everybody > > I have been using GROMACS 2018.1 in the last month and I got an

[gmx-users] how to generate average structure from trajectory

Dear Gromacs users I want to get the average structure of a 10ns simulation by discarding earlier 1ns run. What is the best way to get the average structure? Thanks in advance. Sadaf -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-U

[gmx-users] 12 bead mapping of lipid

How, The mapping that is available for POPS lipid contains 13 beads. But I think the newest mapping has 12 bead. I am wondering how can I get this? Thanks. Rabeta Yeasmin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List be

Re: [gmx-users] 12 bead mapping of lipid

I believe you are looking for Martini CG models. You should be able to download the itp file for all Martini lipids here: http://cgmartini.nl/index.php/force-field-parameters/lipids It has old and current itp files. I think the 'current' file has 12 beads for POPS you are looking for. On Thu, Mar

[gmx-users] Regarding use of harmonic wall model

Hello everyone, I want to use harmonic wall model in gromacs. So, I have generated an input file using charmm-gui and and using its production file (production.mdp) to run the simulation but i am getting that how can use harmonic wall model in it. My want to make gap between beta-barrel where i wan

[gmx-users] mdp option periodic molecules

Dear all, could you please confirm if I understood the periodic molecules entry (I already browsed through the manual and mailing list): I need "periodic molecules = yes", if a molecule interacts=connects to itself via covalent bonds over the periodic boundary. I do NOT need "periodic molec