[gmx-users] ZnO Parameters

> Message: 3 > Date: Fri, 6 Jul 2018 14:39:15 +0300 > From: ali akg?n > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] ZnO Parameters > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Hi, > > You can f?nd parameters on solid state books(for example kittel) Thank you for

Re: [gmx-users] cpu threads in a gpu run

No idea? It seems to be odd. At the beginning of run, I see NOTE: GROMACS was configured without NVML support hence it can not exploit   application clocks of the detected Quadro M2000 GPU to improve performance.   Recompile with the NVML library (compatible with the driver used) or set

[gmx-users] Regarding analysis of dipole-dipole or quadrupole-quadrupole interactions

Dear gmx user, I would like to make analysis of protein system. Is it possible to analyze dipole- dipole or quadruple quadrupole interaction gmx Best regards, Miji -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before po

Re: [gmx-users] y-axis [unit] for gmx analyze -dist command

On 7/9/18 11:38 AM, atb files wrote: Dear users, I have two time series data files - a.xvg and b.xvg. I ran command gmx analyze -f a.xvg -dist aout.xvg gmx analyze -f b.xvg -dist bout.xvg y values for aout.xvg ranges from 0 to 0.05 and that for bout.xvg from 0 to 40, both plots are similar

[gmx-users] y-axis [unit] for gmx analyze -dist command

Dear users, I have two time series data files - a.xvg and b.xvg. I ran command gmx analyze -f a.xvg -dist aout.xvg gmx analyze -f b.xvg -dist bout.xvg y values for aout.xvg ranges from 0 to 0.05 and that for bout.xvg from 0 to 40, both plots are similar to the gaussian distribution. What are the

Re: [gmx-users] gmx trjconv -pbc doesn't work

On 7/9/18 10:20 AM, Chenlin Lu wrote: Hello all, Some of my trajectories has pbc problems. The substrate diffuses out of the pbc box. And I am trying to fix it using gromacs command gmx trjconv -f {}.xtc -s {}.tpr -o {}_nopbc.xtc -pbc nojump. But the fixed trajectories still have same pr

[gmx-users] gmx trjconv -pbc doesn't work

Hello all, Some of my trajectories has pbc problems. The substrate diffuses out of the pbc box. And I am trying to fix it using gromacs command gmx trjconv -f {}.xtc -s {}.tpr -o {}_nopbc.xtc -pbc nojump. But the fixed trajectories still have same problems when I check them in VMD. I caculted

Re: [gmx-users] warming up a protein system

On 7/9/18 4:55 AM, morpheus wrote: Dear Gromacs users, I have a few questions about the warming-up procedure of a simple ~600AA protein in water using the Gromos force field and SPC water. First I do an energy minimization and then I want to warm my protein up to 310K. 1) What does the "cons

Re: [gmx-users] Shell (Drude) model for polarization in GROMACS

On 7/9/18 1:31 AM, Eric Smoll wrote: Thanks Justin, That is very helpful. I can run the water example provided in your paper with the GROMACS "drude" branch. I have built my own tools to construct a core-shell MD topology file for my system. Grompp produces a tpr without complaint but mdru

Re: [gmx-users] MPI

On 7/9/18 2:17 AM, Raag Saluja wrote: Hi! Do you have any tutorials for MPI, please? Check with your system administrator for MPI invocation and syntax. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Bi

Re: [gmx-users] Performing energy minimisation for an alanine scan

Thanks for your help. I completely agree with your points raised. I've dropped the pmx developers and email, hopefully there will be a little bit of wiggle room for me to move forward on this project some time soon. Thanks again, and to Mark and Justin. Anthony Kind regards Anthony Nash PhD

Re: [gmx-users] Performing energy minimisation for an alanine scan

I see your problem. Automating pdb2gmx should be easy if one blindly accepts the protonation states assigned. It does work for most proteins, but I have encountered problematic cases. But, if you notice, weven the pmx web-service seems to use pdb2gmx for generating the topology files. Or else, it r

[gmx-users] Ph.D. candidate position in biomolecular modeling or bioinformatics

Dear colleagues, we have one remaining position for a Ph.D. student interested in molecular simulations of proteins and/or the development of computational tools in the domain of structural bioinformatics to be filled in our laboratory starting in October 2018 or asap hereafter. For details pl

Re: [gmx-users] Performing energy minimisation for an alanine scan

Thanks Abhishek, I'll have to give this some thought when I have some hours to spare. I believe the damage has been done as I already have my 600+ coordinate and respective structures as part of the pmx web-service. With their output I was able to get stright in there with my editconf, genion,

Re: [gmx-users] Performing energy minimisation for an alanine scan

Hello Anthony, I was just looking at this aspect. In the mutres.mtp file try to replace just the [coords] section with this: [ coords ] -2.994 -4.4706.993 -3.510 -5.3327.063 -1.676 -4.4157.600 -1.774 -4.9018.572 -0.668 -5.2346.757 -1.036 -6.2556.6

Re: [gmx-users] Performing energy minimisation for an alanine scan

Hello Abhishek, I think you are onto something there. I've just found the mutres.mtp file. I can understand the idea of simply changing all [X2A] residue topologies but then how do I reflect these changes in the coordinate files? Sorry, this is probably quite simple, I've just stuck between fi

Re: [gmx-users] Performing energy minimisation for an alanine scan

Hello Anthony, Just out of curiosity, I checked the pmx code. It looks like a simple hack into the hybrid residue database (mutres.mtp file, present in the ff directories supplied by the authors) should do the trick. If you look into this file, it contains the full topology and coords for all poss

[gmx-users] cpu threads in a gpu run

Hi, When I run "-nt 16 -nb cpu", I see nearly 1600% cpu utilization. However, when I run "-nt 16 -nb gpu", I see about 600% cpu utilization. Is there any reason about that? I want to know with the cpu threads in a gpu run is controllable. Regards, Mahmood -- Gromacs Users mailing list * Pleas

[gmx-users] warming up a protein system

Dear Gromacs users, I have a few questions about the warming-up procedure of a simple ~600AA protein in water using the Gromos force field and SPC water. First I do an energy minimization and then I want to warm my protein up to 310K. 1) What does the "constraints = all-bonds" mean exactly? In t