[gmx-users] Query regarding Preferential Interaction Coefficient Calculation

Dear all, I have done the MD simulation of protein in osmolytes, now i want to calculate the preferential interaction coefficient of osmolytes from protein surface.Will anyone please guide me the proper steps of the calculation? Thanks and regards -- Ishrat Jahan Research Scholar Department Of

[gmx-users] query regarding state.cpt file

MD_output.tar.gz Greetings Sir/Madam I am running MD simulation using commands listed below-

Re: [gmx-users] regarding editconf

My advice is that don't use many option in on shot. In place of -center try by -translate with rotation. Best regard On Tue, Jan 15, 2019 at 8:52 PM Ali Khodayari < ali.khoday...@student.kuleuven.be> wrote: > Thank you Justin. I try to search more for the reason. My best, Ali > > -Original

[gmx-users] Regarding self-assembly of Peptides

Hi, I have a peptide (capped peptide) and i want to do the self assembly in GROMACS. So, may i know how to do this self assembly in gromacs..?? Any suggestions..? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] GROMACS Infrastructure

Hello GROMACS Users, My name is Nam and I support a campus supercomputer for which one of the major applications is GROMACS. I was curious if anyone has optimized servers for cost and has a blueprint for that, what servers and configurations are ideal for cost and performance? -- Nam Pho

[gmx-users] Calculating distance between solute and solid surface

Hello GMX users, I'm simulating a polymer in water on a solid surface. I'm trying to calculate the dynamic distance between polymer monomers and the surface (top layer of the surface). My reference is the surface and I used this command gmx distance -f NVT.xtc -s NVT.tpr -selrpos atom -seltype

[gmx-users] Use all-atom PDB or coarse-grained PDB as the restraints for grompp a coarse-grained gro?

In Gromacs 2018, -r is used to provide the restraint file for grompp. I have a grompp command used for a coarse-grained (CG) gro file, i.e. CG.gro: gmx grompp -f parameter.mdp -r AllAtom.pdb/CG.pdb -c CG.gro -p system.top -o MD.tpr So in the command above, should I use AllAtom.pdb or CG.pdb

Re: [gmx-users] core dumped

Hello; Thank you Justin for your answer. I have mailed fe2o3.pdb file in this gmail for you. in atomname2type.n2t, for Fe-O bonds, I have used Fe type From the atomtype.atp of charmm36 force field, : (FE 55.84700 ; heme iron 56) is it correct? On Tue, Jan 15, 2019 at 5:30 PM

Re: [gmx-users] Single precision enough for MD of peptide?

On 1/15/19 10:39 AM, Neena Susan Eappen wrote: Hi Justin, Thank you. What is the solution for this? Solution to what? -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech

Re: [gmx-users] Single precision enough for MD of peptide?

Hi Justin, Thank you. What is the solution for this? Neena From: Neena Susan Eappen Sent: Saturday, January 12, 2019 3:15:11 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Single precision enough for MD of peptide? Hi GMX users, I

Re: [gmx-users] regarding editconf

Thank you Justin. I try to search more for the reason. My best, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Justin Lemkul Sent: dinsdag 15 januari 2019 16:10 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] regarding editconf On

Re: [gmx-users] regarding editconf

On 1/15/19 9:34 AM, Ali Khodayari wrote: Thank you for your response Justin! I don't really see how it can cause an error, while it might be just a visualization defect in VMD. Previously, I tried to perform each step separately, like doing a centering by -center 0 0 0, but even performing

Re: [gmx-users] regarding editconf

Thank you for your response Justin! I don't really see how it can cause an error, while it might be just a visualization defect in VMD. Previously, I tried to perform each step separately, like doing a centering by -center 0 0 0, but even performing this step leads to the error "step 0: Water

Re: [gmx-users] regarding editconf

On 1/15/19 7:46 AM, Ali Khodayari wrote: Dear users, I am trying to reorient and re-center my solute using editconf. Performing such I can place the structure at the desired place, yet it is outside the box when I visualize it in VMD. It leads to an error after mdrun complaining about a

Re: [gmx-users] core dumped

On 1/15/19 6:47 AM, rabee khorram wrote: Segmentation fault (core dumped)? *Hello everyone, I am runnig nano Fe2O3 structure with PEN drug with gromacs5.* How did you parametrize and validate these species? *but in step :* * gmx mdrun -v -deffnm nvt * * I am getting an error : step

Re: [gmx-users] Conversion CHARMM FF to Gromos54a7 FF

On 1/14/19 11:28 AM, Salman Zarrini wrote: Dear all, I have a CHARMM all atoms force fields for a solid with limited atom types, and I want to convert them to Gromos54a7 force fields. Would you please confirm that below are the changes I should make to do so? 1. Combination rule # 2 is used

Re: [gmx-users] How To Calculate The Energy From The Coordinates Of Pdb File?

On 1/14/19 3:10 AM, Mehdi Mirzaie wrote: Dear Groamcs User, I would be appreciated if you guide me, how to extract pairwise energy (between residues) from the coordinates of PDB file? Since the Pdb files are already minimized, obviously, there is no needed to run energy minimization step.

Re: [gmx-users] Single precision enough for MD of peptide?

On 1/12/19 10:15 AM, Neena Susan Eappen wrote: Hi GMX users, I just installed GROMACS 2018.4 on my windows PC without GPU support. My PC is capable of only single precision with a 64-bit memory, would this affect the trajectory of my peptide? Nearly all conventional MD simulations are

Re: [gmx-users] Energy cal from MD simulations

On 1/12/19 1:10 AM, Lod King wrote: Hi, I have obtained a 100 ns simulation using Amber. I would like to calculate the potential energy (VDW, COUL,ect) from the trajectory, below is my command. $gmx grompp -f test.mdp -p ../gromacs.top -n ../index.ndx -c ../300.pdb -o rerun.tpr -maxwarn 1

Re: [gmx-users] gmx 2019 performance issues

Thanks for the inputs! * I will go with the cheaper CPU * I am looking forward to the gpu-only gromacs; impatiently On 01/15/2019 01:55 PM, Mark Abraham wrote: Hi, On Tue, Jan 15, 2019 at 1:30 PM Tamas Hegedus wrote: Hi, I do not really see an increased performance with gmx 2019 using

Re: [gmx-users] gmx 2019 performance issues

Hi, On Tue, Jan 15, 2019 at 1:30 PM Tamas Hegedus wrote: > Hi, > > I do not really see an increased performance with gmx 2019 using -bonded > gpu. I do not see what I miss or misunderstand. > Unfortunately that is expected in some cases, see

[gmx-users] regarding editconf

Dear users, I am trying to reorient and re-center my solute using editconf. Performing such I can place the structure at the desired place, yet it is outside the box when I visualize it in VMD. It leads to an error after mdrun complaining about a water molecule not being settled. Here is the

[gmx-users] gmx 2019 performance issues

Hi, I do not really see an increased performance with gmx 2019 using -bonded gpu. I do not see what I miss or misunderstand. The only thing I see that all cpu run at ~100% with gmx2018, while some of the cpus run only at ~60% with gmx2019. There are: 196382 Atoms Speeds comes from 500 ps

Re: [gmx-users] gmx 2019 running problems

Hi, Thanks for the feed-backs. Yes, I could build gmx 2019 on a hosts running with nvidia driver 4.10 Tamas On 01/14/2019 09:06 PM, Tamas Hegedus wrote: Hi, I tried to install and use gmx 2019 on a single node computer with 4 GPUs. I think that the build was ok, but the running is... There

[gmx-users] core dumped

Segmentation fault (core dumped)? *Hello everyone, I am runnig nano Fe2O3 structure with PEN drug with gromacs5.* *but in step :* * gmx mdrun -v -deffnm nvt * * I am getting an error : step 2600, remaining wall clock time: 60 s Segmentation fault (core dumped)* *and don't create nvt.gro.!*