Re: [gmx-users] Set up anti parallel membrane system for CompEL simulation

Hi Jochen, Thank you for the suggestions. Best, Zheng On Mon, May 4, 2020 at 5:24 PM Jochen Hub wrote: > > > Am 04.05.20 um 23:21 schrieb Jochen Hub: > > > > > > Am 04.05.20 um 21:33 schrieb Zheng Ruan: > >> Hi, > >> > >> I'm tryi

[gmx-users] Set up anti parallel membrane system for CompEL simulation

Hi, I'm trying to setup an antiparallel membrane system for CompEL simulation. It is relatively straightforward to convert an existing single membrane system to a parallel system by using # gmx genconf -f system.gro -nbox 1 1 2 -o system.parallel.gro However, is there an easy way to invert one

Re: [gmx-users] Decrease position restraints force constant on the fly

Hi Dawid, If I understand correctly, you may able to control the restraint using plumed. Check the "Moving on a more complex path" in this tutorial ( https://plumed.github.io/doc-v2.3/user-doc/html/belfast-5.html). Ruan On Mon, Mar 12, 2018 at 10:38 AM, Justin Lemkul wrote: >

Re: [gmx-users] phi/psi

Hi, g_chi has -rama, -phi, and -psi option for this. Ruan On Fri, Jan 12, 2018 at 10:11 AM, João Henriques wrote: > Hello, > > Don't know if there's a native gromacs tool to do so, but I'd use PLUMED > for this sort of thing: >

Re: [gmx-users] situation where ligand is connected to amino acid

Hi Ming and Justin, I have the same situation in which my protein has a cysteine residue covalently linked to a drug. I'm regularly using amber99sb-ildn force field. Is there existing tools that can help parameterize the modified residue? Thank you! Ruan On Tue, Jan 2, 2018 at 8:04 PM, Justin

[gmx-users] How to correctly setup gmx_mpi mdrun

Hi Gromacs Users, I'm learning how to run a simple replica exchange MD simulation on my own computer. My computer has 12 Xeon E5-2630 CPUs and 1 GeForce GTX 770 GPU. I used to compile gromacs without the -DGMX_MPI option and it runs fine for normal MD. I can control the number of CPUs to use by

Re: [gmx-users] Gromacs Simulation Question

Hi, You find find this paper relevant ( https://www.ncbi.nlm.nih.gov/pubmed/22034434). Ruan On Fri, Jan 6, 2017 at 5:14 PM, Academic Research wrote: > Hello everyone, > > > I have computationally designed several synthetic proteins that are not > found in nature. > > >

Re: [gmx-users] Protonation state of phospho-tyrosine in neutral PH

Hi Justin, Thank you! Based on the PKa value, I will go with the double protonated P-Tyr for my purpose, since the PKa1 and PKa2 for the PO3 in P-Tyr are 2 and 5.8 respectively. Ruan On Fri, Dec 23, 2016 at 1:15 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/22/16 10:52

[gmx-users] Protonation state of phospho-tyrosine in neutral PH

Hi Gromacs Users, I'm trying to run simulation on a protein with phosphorylated tyrosine residues. The amber force field parameters (http://research.bmh. manchester.ac.uk/bryce/amber) provides three different protonation states of the phospho-tyrosine residue. What is the predominant form of

Re: [gmx-users] pdb2gmx assign CSER to non-terminal serine

Thank you Justin!!! That's the problem. Now everything runs well. Ruan On Tue, May 3, 2016 at 12:04 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/3/16 12:02 PM, Zheng Ruan wrote: > >> Hi Gromacs Users, >> >> I'm using pdb2gmx to process my pdb fi

[gmx-users] pdb2gmx assign CSER to non-terminal serine

Hi Gromacs Users, I'm using pdb2gmx to process my pdb files with a phospho-tyrosine using amber99sb-ildn.ff. The relavant content in my pdb looks like this (There is a serine before phosphorylated tyrosine): ATOM202 N SER26 31.593 -68.669 -25.834 1.00208.96 N ATOM203 CA

Re: [gmx-users] Huge conformational change of ATP molecules

gy/Periodic_Boundary_Conditions > > Mark > > On Tue, Feb 23, 2016 at 6:18 AM Zheng Ruan <zruan1...@gmail.com> wrote: > > > Hi Gromacs Users, > > > > I'm running 20ns MD simulation of a protein kinase with ATP bond. I use > > amber99sb-ildn force field with para

[gmx-users] Huge conformational change of ATP molecules

Hi Gromacs Users, I'm running 20ns MD simulation of a protein kinase with ATP bond. I use amber99sb-ildn force field with parameters of ATP derived from the database of Richard Bryce. What surprised me is that the ATP molecules displays a huge flexibility and conformational change. First, it

[gmx-users] Not sure how to include dihedral angle params of ATP into force field

should I do to put the params in the param table to ffbonded.itp? Thank you! Zheng Ruan -- 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

[gmx-users] Tesla K40 and K80 performance for Gromacs

Hi gromacs users, Our lab decides to buy some exclusive computational resources for MD using gromacs. The HPC center in our university offers 2 options. I guess some of you are using K80 GPU right now so I'd like to hear your suggestions/experiences about it. option 1 (Tesla K40): * Dual Intel

[gmx-users] hbond correspondence between hbond.log and hbmap.xpm

by g_hbond doesn't seems to be consistent with those found by pymol. Thank you! Zheng Ruan -- 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