Re: [gmx-users] FEP calculations on multiple nodes

Hi, It is intended that they work on GPUs, but the implementation of FEP support for FB restraints pre-dates GPUs for nonbonded interactions, and is probably not tested, so could be broken. Mark On Thu, 24 Aug 2017 18:03 Vikas Dubey wrote: > Hi, > I am also running calculation on GPUs. If FB r

[gmx-users] Gromacs simulation of two or more peptide chain

Dear all, I would like to run an MD simulation for two or more peptide chain. I got the following error in the steepest descent energy minimization step. Could you please suggest me, how can I do the MD simulation? Steepest Descents: Tolerance (Fmax) = 1.0e+02 Number of steps=

Re: [gmx-users] FEP calculations on multiple nodes

Hi, I am also running calculation on GPUs. If FB restraints are only limited to CPUs, I am sorry I was not aware of that. On 24 August 2017 at 17:55, Mark Abraham wrote: > Hi, > > Thanks. That should not be the problem, because all such computations are > only on the CPU... But hopefully we will

Re: [gmx-users] FEP calculations on multiple nodes

Hi, Thanks. That should not be the problem, because all such computations are only on the CPU... But hopefully we will see. Mark On Thu, 24 Aug 2017 17:35 Leandro Bortot wrote: > Hello all, > > This may add something: I had Segmentation Fault using flat-bottom > restraints with GPUs befor

Re: [gmx-users] FEP calculations on multiple nodes

Hello all, This may add something: I had Segmentation Fault using flat-bottom restraints with GPUs before. I just assumed that this type of restraint was not supported by GPUs and moved to a CPU-only system. Sadly it was some time ago and I don't have the files anymore. Best, Leandro

Re: [gmx-users] FEP calculations on multiple nodes

Hi, Thanks. Good lesson here - try simplifying until things work. That does suggest there is a bug in flat bottomed position restraints. Can you please upload a tpr with those restraints, along with a report at https://redmine.gromacs.org so we can reproduce and hopefully fix it? Mark On Thu, 24

Re: [gmx-users] FEP calculations on multiple nodes

Hi, I have just checked with normal restraints. it works fine. Simulation crash with flat bottom restraints. On 24 August 2017 at 16:43, Mark Abraham wrote: > Hi, > > Does it work if you just have the normal position restraints, or just have > the flat-bottom restraints? In particular, I could

Re: [gmx-users] Regarding Atom in residue XXX was not found in rtp entry with xxx atoms while sorting atoms

Hi, pdb2gmx is giving you the normal termini found in a peptide in aqueous solution near physiological pH, ie. zwitterionic. You can choose different termini if your force field supports it, but you should only do so if you are modelling something that requires a non-zwitterionic form. Mark On T

Re: [gmx-users] FEP calculations on multiple nodes

Hi, Does it work if you just have the normal position restraints, or just have the flat-bottom restraints? In particular, I could image the latter are not widely used and might have a bug. Mark On Thu, Aug 24, 2017 at 4:36 PM Vikas Dubey wrote: > Hi everyone, > > I have found out that position

Re: [gmx-users] FEP calculations on multiple nodes

Hi everyone, I have found out that positions restrains is the issue in my FEP simulation. As soon as I switch off position restraints it works fine. I have the following the restraint file for the ions in my system (I don't see any problems with it): *[ position_restrai

[gmx-users] Regarding Atom in residue XXX was not found in rtp entry with xxx atoms while sorting atoms

Hello, I have a amino acid and i am using charmm 36 FF to create the topology by:- gmx pdb2gmx -f abc.pdb -o abc.grobut i am getting error as:- Atom HO in residue XXX was not found in rtp entry with xxx atoms while sorting atoms. So if i use the -ignh flag in the gmx pdb2gmx command, i am ge

Re: [gmx-users] Torsion analysis

gmx chi? http://manual.gromacs.org/documentation/2016.3/onlinehelp/gmx-chi.html I never used it though. I personally like to use PLUMED for this: https://plumed.github.io/doc-v2.3/user-doc/html/_t_o_r_s_i_o_n.html João On Thu, Aug 24, 2017 at 1:43 PM, RAHUL SURESH wrote: > Dear All, > > To d

[gmx-users] Torsion analysis

Dear All, To deduce the the stability of ligand and protein binding, I would like to carry out torsion analysis. How is it possible using Gromacs? Thanks in advance -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please searc

[gmx-users] FEP: mdp setting for mutation

Hi, Following changes are made in the mdp file for mutation analysis.Can anyone tell me is there anything wrong here? ; init_lambda_state0123456789 10 11 12 13 14 15 16 17 18 19 20 vdw_lambdas = 0.00 0.05 0.10 0.15 0.

Re: [gmx-users] g_cluster

Dear Nikolai, Group 1. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se On 24 Aug 2017, at 00:07,

Re: [gmx-users] Average and bfactors.pdb

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear justin Thanks alot for your advice  Sent from Yahoo Mail for iPhone On Thursday, August 24, 2017, 5:51 AM, Justin Lemkul