[gmx-users] tpo is removed in simulation

respected sir 5.0.7 43A1p my TPO is removed in simulation while sep is remain attached with residue ??? kindly privide me any guide line -- 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

[gmx-users] Distance between two specific residues

Dear Gromacs users, I am trying to calculate distance between two specific residues of active site of my protein in MD. I have made separate .index file of  two specific groups. Then I am trying this command " gmx distance -f md_0_1.xtc -s md_0_1.tpr -oav distance.xvg -select -n index.ndx -tu n

[gmx-users] tpo is removed after 10ns... help help plz

respected sir! version 5.0.7 43A1p respected sir kindly provide me guide line about TPO my TPO is breakdown when i generated PDB of my protein while SEP and PTR is remain attached i am surprised what happens with TPO ??? kindly provide me any idea what happens TPO?? why its breakdown ??? thank

[gmx-users] How Gromacs H_bond module compute hydrogen bonding correlation function practically and in detail?

Dear all gromacs users and developers I make my own code based on definition introduced on paper of Luzar, Chandler and Van der Spoel and compute correlation function so that It can have initial value of 1 and approach to 0 as time goes on. I plot computed correlation function together with co

[gmx-users] The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element

Hello, i ḿ working in a lipid bilayer using charmm36 forcefield and trying to do NVT equilibration but when i use grompp for nvt i receive the folowing error: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size o

Re: [gmx-users] gpu-performance reduces during FEP calculation

Hi It is a small ligand decoupling from its native protein and there are orientational restraints near high decoupled region. I am using gcc and gfortran compilers . Jagannath On Tue, Mar 15, 2016 at 6:54 PM, Szilárd Páll wrote: > No, the free energy kernels run on the CPU. This large change m

Re: [gmx-users] Problem with the mdrun_openmpi on cluster

assuming that below command produce what I am looking for -bash-4.1$ tail -n 3 eq_npt.log (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 1978.319102.192 21.487 1.117 Finished mdrun on node 0 Tue Mar 15 16:23:03 2016 what combination of the shell commands wil

Re: [gmx-users] Problem with the mdrun_openmpi on cluster

Right, thanks so much! 2016-03-15 13:58 GMT+01:00 Mark Abraham : > Hi, > > > On Tue, Mar 15, 2016 at 11:57 AM James Starlight > wrote: > >> just performed some benchmarks with full atomic system- short md of >> the water soluble protein still using mpiexec -np 46 mdrun_openmpi of >> the GMX 4.5 a

Re: [gmx-users] gpu-performance reduces during FEP calculation

No, the free energy kernels run on the CPU. This large change must mean that you have a relatively large fraction of the system participating in perturbed interactions. What compiler are you using? The free energy kernel is a bit "sensitive" (to put it mildly) and I do remember seeing much better

[gmx-users] gpu-performance reduces during FEP calculation

Dear Gromacs users I am trying to perform Free energy peturbation calculation in presence of distance, angle and dihedral-restraint for a protein-ligand system. However, I am finding, on turning on the FEP calculation, the performance of gromacs5.1.1. in a gpu-based workstation significantly gets

Re: [gmx-users] Problem with the mdrun_openmpi on cluster

Hi, On Tue, Mar 15, 2016 at 11:57 AM James Starlight wrote: > just performed some benchmarks with full atomic system- short md of > the water soluble protein still using mpiexec -np 46 mdrun_openmpi of > the GMX 4.5 and there were no such errors with DD so it seems that the > problem indeed in

Re: [gmx-users] Fourier dihedral potential: typo or correct?

Hi, Yes, that's a typo. I have fixed it for future versions. Mark On Tue, Mar 15, 2016 at 1:49 AM Parvez Mh wrote: > Dear all: > > In manual-5.06, page:82, > > > [image: Inline image 1] > Shouldn't the last term be C4(1-cos(4Phi)) ? > > --Masrul > -- > Gromacs Users mailing list > > * Please s

[gmx-users] QMmethod

Hi,   a short question regarding the mdp option "QMmethod" when using ORCA for QM/MM simulations. If I understand the source code (gromacs/mdlib/qm_orca.cpp) of the ORCA interface correctly, it looks like GROMACS is not telling ORCA what QMmethod to use.  Does the QMmethod mdp-option change anyt

Re: [gmx-users] Problem with the mdrun_openmpi on cluster

just performed some benchmarks with full atomic system- short md of the water soluble protein still using mpiexec -np 46 mdrun_openmpi of the GMX 4.5 and there were no such errors with DD so it seems that the problem indeed in MARTINI atoms representation. BTW how I could quickly check some info a

Re: [gmx-users] How Gromacs h_bond module compute hydrogen correlation function ?

Hi again, I had a look at your post at ResearchGate, where you ask the same question and provide both source code and output from your. Two things differ between gromacs’ calculation and yours. First of all, gromacs normalises the correlation function so that it is 1 at t=0. This is common prac

Re: [gmx-users] Trajectory correction for pbc before H-bond analysis

Dear Agnivo, No. g_hbond / gmx bond takes pbc into account, so you normally don’t need to bother with preprocessing your trajectory. Kind regards, Erik > On 15 Mar 2016, at 01:09, Agnivo Gosai wrote: > > Dear Users, > > I always do pbc correction for the trajectory before doing RMSD, Radius

Re: [gmx-users] Query regarding energy minimization step (step 12: Water molecule starting at atom 13529 can not be settled.)

Dear all gromacs users, I am trying to run simulation for my Phophorylated threonin (​​TPO at 172 position in A chain og 4CFF pdb id), I have generate topology using Prodrg2server. Then i try to run energy minimization step its showing following error-- 1.