Re: [gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field

On 11/30/15 3:17 PM, Rakesh Ramachandran wrote: Hi Justin, Thanks for the reply. I have few more doubts. I had mentioned CHARMM27 just for consistency with Gromacs naming. In the website it mentions that those settings are for CHARMM36 and I read at lot of places that this force field is

Re: [gmx-users] how to make .trr file readable

On 12/1/15 8:11 AM, Ayesha Kanwal wrote: Dear Bipin Singh, i had read MDAnalysis but i could not get it to how make .trr file readable . could you provide me an easy tutorial ? or number of steps to which i can easily follow it and make .trr readable. or there is any source code which i can

Re: [gmx-users] LINC warning after long time simulations

On 11/30/15 5:01 PM, 凌未风 wrote: Hi All: I pasted this once several days ago but no one replied. I know there are a lot of questions in the forum regarding LINC warning, but my problem seems quite strange. So I write here again. My simulation system contains lipids and proteins, I am using

[gmx-users] how to make .trr file readable

Dear Gromacs experts, i am very new to Gromacs i only want to take .trr file and make it readable . as i want to use .trr file in my own tool as an input format. how can i make it readable and can use it in my tool ? Best regards Ayesha -- Gromacs

Re: [gmx-users] Equilibration fails only when run from script

On 12/1/15 6:39 AM, R Corey wrote: Hello I am running a series of FEP MD simulations using Gromacs 5.0.4, for each a steepest descents minimization, NVT equil, NPT equil and production run, all controlled by a central script. However, only about 50% of the runs get through the NVT

Re: [gmx-users] atom numbering

On 12/1/15 7:38 AM, Marta Wisniewska wrote: Dear Gromacs users, My problem focus on number order. I am preparing my system to md. In my pdb file I made a some modifications (delete chains or ligand compounds). During preparation of topology and gro file, the residue number ordering is

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

Dear Hannes, > I have some trouble reading your top file in my web browser Apologies, am not sure if this works in this list, but I am now also attaching my topol.top and grompp.mdp files. I hope this let's you see better what I am doing wrong. > As your two dummy types appear to be identical >

Re: [gmx-users] how to make .trr file readable

http://manual.gromacs.org/online/trr.html Peter -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of bipin singh Sent: Tuesday, December 01, 2015 2:48 PM To: Discussion list for GROMACS users

Re: [gmx-users] how to make .trr file readable

Dear Bipin Singh, i had read MDAnalysis but i could not get it to how make .trr file readable . could you provide me an easy tutorial ? or number of steps to which i can easily follow it and make .trr readable. or there is any source code which i can use for reading this file. > Date: Tue, 1

[gmx-users] Equilibration fails only when run from script

Hello I am running a series of FEP MD simulations using Gromacs 5.0.4, for each a steepest descents minimization, NVT equil, NPT equil and production run, all controlled by a central script. However, only about 50% of the runs get through the NVT equilibration without crashing - crash error as

[gmx-users] atom numbering

Dear Gromacs users, My problem focus on number order. I am preparing my system to md. In my pdb file I made a some modifications (delete chains or ligand compounds). During preparation of topology and gro file, the residue number ordering is changed. Is there any possibility to preserve number

Re: [gmx-users] extracting coordinates from traj.xtc

On 12/1/15 2:04 AM, mah maz wrote: Dear all, I have some problems extracting data from traj.xtc. The command " g_traj -s -ox" doesn't give reasonable coordinates. I tried "trjconv" but again Why aren't they reasonable? That also couldn't have been your command, which requires at least a

Re: [gmx-users] how to make .trr file readable

http://pythonhosted.org/MDAnalysis/documentation_pages/coordinates/TRR.html -- Thanks and Regards, Bipin Singh On Tue, Dec 1, 2015 at 6:10 PM, Ayesha Kanwal wrote: > Dear Gromacs experts, > i am very new to Gromacs i only want to take

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

You still have couple-moltype set. On Tue, 1 Dec 2015 15:39:40 +0100 Sebastian Stolzenberg wrote: > OK, thanks a lot, Hannes, > > I combined the "CL-" and "NA+" into one "NC" [moleculetype] and > switched off the couple-* switches as you suggested (attached), > but

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

OK, thanks a lot, Hannes, I combined the "CL-" and "NA+" into one "NC" [moleculetype] and switched off the couple-* switches as you suggested (attached), but I am still receiving the same warning message: "The lambda=0 and lambda=1 states for coupling are identical" I guess I am almost there, am

Re: [gmx-users] extracting coordinates from traj.xtc

Thank you Justin. I expected that only water molecules are written in .xtc but all the others are there! g_traj -f traj.xtc -ox gives numbers like 1.64e-318 for all frames! How can I get real coordinates from .xtc? Thanks! On Tue, Dec 1, 2015 at 10:34 AM, mah maz wrote: >

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

Ok, my attachment seems to have been stripped, so inline only. Hope it's not too bad. [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb DU DU 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. OW OW 0.0 0.0

Re: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?

Dear Sebastian, I have got your attachment. I do not know all intricacies of Gromacs but for relative free energies you only use one moleculetype for the perturbed group, see attachment. You do not use the couple-* switches for relative simulations. Yes, you are right about typeA and typeB.

Re: [gmx-users] LINC warning after long time simulations

A few things to check when trying to figure out the origin of the LINCS error that occurs only after a long run: 1) What is your time step? 2) If you restart from a previous checkpoint does the same error occur? 3) What are your LINCS settings? 4) Do you see any unphysical behavior prior to the