[gmx-users] Why charge parameter of cations like Cu2+, Zn2+ in GROMOS 54a7 force field in GROMACS equals to zero?

Hi All the the values in the charge column in the ffnonbonded.itp are not used by GROMACS and remain present for history reasons (and probably for compatibility with older GROMACS versions). The charges for each residue/molecules are now in the rtp. Best Stéphane

[gmx-users] bonded interaction larger than cutoff

Dear all, I add a harmonic bond between two ends of my molecule (then my molecule will have circle shape) with hope to calculate the force opens my molecule (force the molecule straight). Unfortunately, when this bond is quite big, gromacs said this bonded interaction could not be calculated. How c

Re: [gmx-users] Epsilon_r

On Mon, Dec 17, 2018 at 1:49 AM Shan Jayasinghe < shanjayasinghe2...@gmail.com> wrote: > Dear Gromacs Users, > > How do we determine the epsilon_r for a MD simulation? If we do a MD > simulation for a system with some molecules in water, what is the value for > epsilon_r? Is it equal to the relati

Re: [gmx-users] bonded interaction larger than cutoff

On Mon, Dec 17, 2018 at 7:48 AM Quyen Vu Van wrote: > Dear all, > I add a harmonic bond between two ends of my molecule (then my molecule > will have circle shape) with hope to calculate the force opens my molecule > (force the molecule straight). > Unfortunately, when this bond is quite big, gro

[gmx-users] contact analysis within the all backbone of a protein

hi, to calculate the contact between the all backbone of a protein ,is the following command is correct gmx mindist -f dynamic.xtc -s equilibration.gro -n bb-p.ndx -dt 1000 -d 0.5 -on contact.xvg -od mindist.xvg because after entering this command i have to select the same group for two times. U

[gmx-users] Running simulation differences

Dear Gromacs users, I have tried to run twice the same simulation (same .tpr input file) in the same workstation, but the results I obtain significantly differ, for example: (-276.96 ± 40.7 kj/mol) and (-257.25 ± 35.86 kj/mol). Are these differences normal? As these results are different, how

Re: [gmx-users] Running simulation differences

Hi, First, with those associated errors I wouldn't say that those differences are significant. More to your question, Gromacs simulations with default parameters are not generally reproducible. See the last 2 points in this section of the reference manaul: http://manual.gromacs.org/current/user-g

Re: [gmx-users] Running simulation differences

Hi Kevin, Thank you very much for your answer. Do you know how I can set the "double precision"? C. -Mensaje original- De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se En nombre de Kevin Boyd Enviado el: lunes, 17 de diciembre de 2018 16:03 Para: gmx-us...@gromacs.org Asunto: Re:

Re: [gmx-users] Running simulation differences

On Mon, Dec 17, 2018 at 10:15 AM Gonzalez Fernandez, Cristina < cristina.gonzalezf...@unican.es> wrote: > Hi Kevin, > > Thank you very much for your answer. Do you know how I can set the "double > precision"? > > You would have to recompile and reinstall with the appropriate option given to CMake.

Re: [gmx-users] Running simulation differences

Thank you very much Justin for your suggestions. C. -Mensaje original- De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se En nombre de Justin Lemkul Enviado el: lunes, 17 de diciembre de 2018 16:18 Para: Discussion list for GROMACS users Asunto: Re: [gmx-users] Running simulation di

Re: [gmx-users] gromacs 2018 with OpenMPI + OpenMP

On Sun, Dec 16, 2018 at 12:16 PM Deepak Porwal wrote: > > Are you sure that's better than mdrun's internal thread binding? > yes even with warnings I see better performance, so surely if we can remove > warnings Which warnings are you referring to? > and bind properly I'm curious, can you e

Re: [gmx-users] using dual CPU's

On Thu, Dec 13, 2018 at 10:12 PM wrote: > Szilard, > > I get an "unknown command " gpustasks in : > > 'mdrun -ntmpi N -npme 1 -nb gpu -pme gpu -gpustasks TASKSTRING > TASKSTRIGS is a placeholder. It is the manual mapping of tasks to GPU hardware. > > where > typically N = 4, 6, 8 are worth a

Re: [gmx-users] using dual CPU's

On Thu, Dec 13, 2018 at 8:39 PM p buscemi wrote: > Carsten > > thanks for the suggestion. > Is it necessary to use the MPI version for gromacs when using multdir? - > now have the single node version loaded. > Yes. > I'm hammering out the first 2080ti with the 32 core AMD. results are not > st

Re: [gmx-users] using dual CPU's

Thank you again, "I'll be back" when I sort all this out. Paul -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Szilárd Páll Sent: Monday, December 17, 2018 1:16 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] using dual CPU

[gmx-users] scale interactions between two groups of atoms

Dear Gromacs experts, In Gromacs, is there some way to scale the pairwise nonbonded interactions between two sets of atoms by some lambda value and compute the associated free energy change? The two groups of atoms are on two molecules. CHARMM has the BLOCK utility that can do this but it's unc

[gmx-users] Residue DAN always renamed to DNA

Are the GROMACS scripts meant to rename residues when processing? I have one that is called DAN, and it is always changed to DNA, whether need to select a group and haven't passed an .ndx file but using a .tpr file, or for an example of processing by make_ndx, see ... https://twitter.com/dr_dbw/s

Re: [gmx-users] Residue DAN always renamed to DNA

On Mon, Dec 17, 2018 at 8:17 PM Dallas Warren wrote: > Are the GROMACS scripts meant to rename residues when processing? I have > one that is called DAN, and it is always changed to DNA, whether need to > select a group and haven't passed an .ndx file but using a .tpr file, or > for an example o

Re: [gmx-users] Residue DAN always renamed to DNA

Looking into that now, thanks. Yes, it is listed as being DNA, but the residue DAN is no longer listed as a possible selection. So it means that with external scripts you can't select based on the residue name "DAN". Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Ins

Re: [gmx-users] Residue DAN always renamed to DNA

Line 152 of residuetypes.dat (located in the share/gromacs/top directory) has: DAN DNA If I remove that line, then it no longer changes it to DNA and now lists it as a stand alone residue that you can select. Cheers. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash

Re: [gmx-users] contact analysis within the all backbone of a protein

can anyone please tell me is this correct or how i can do this. On 12/17/18, SHAHEE ISLAM wrote: > hi, > to calculate the contact between the all backbone of a protein ,is the > following command is correct > gmx mindist -f dynamic.xtc -s equilibration.gro -n bb-p.ndx -dt 1000 > -d 0.5 -on conta

[gmx-users] Protein-ligand complex simulation and ATBserver file

Dear all, I have started following the new tutorial and the old tutorial to carryout the simulation of JZ4 with Lysozyme. I was unable to run the cgen

[gmx-users] contact analysis between the all backbone of same protein

hi, to calculate the contact between the all backbone of a protein ,is the following command is correct gmx mindist -f dynamic.xtc -s equilibration.gro -n bb-p.ndx -dt 1000 -d 0.5 -on contact.xvg -od mindist.xvg because after entering this command i have to select the same group for two times. U