[gmx-users] 回复: Re: Implicit Solvent and Box Size

Dear Justin, I have tried implicit solvent without pbc or barostat. The box was not compressed but the molecules flew out of the box. I believe that it was because of nopbc box. Would you please give more information on why implicit solvent is used without pbc? Thanks！ Regards, Zhuo --

Re: [gmx-users] Shape of the aggregate

First thing is that GROMACS measures things in nanometers, whereas VMD uses Angstroms. Other thing to check is whether the first and last atom in the index group selected when using polystat is the same as the two atoms you selected in VMD. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition

Re: [gmx-users] Solvation of protein on membrane surface .JPG

A visual artefact of the periodic boundary condition. See https://twitter.com/dr_dbw/status/909559339366572032 Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052

[gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers

Hello Gromacs Developers/Users, I'm trying to install Gromacs-2019.3 on Intel Xeon W-2175 with Intel compilers (+MKL+MPI). First I compiled cmake with Intel compilers. All output files are attached. cmake, make seemed to go ok, but all check test failed. What do I do wrong?

Re: [gmx-users] Implicit Solvent and Box Size

Dear Justin, Thank you for your suggestions! So what I have done is right. For implicit solvent, I just need turn on the options in .mdp file and no .itp file is needed to be included in the topology file. (I have tried but get errors). Thanks! Regards, Zhuo -- Gromacs Users mailing list *

Re: [gmx-users] Solvation of protein on membrane surface

On 10/7/19 3:30 AM, Olga Press wrote: Dear all, I would like to perform a simulation of protein on a membrane surface. Following the placement of the protein on the DOPC surface I solvated the system by the following command: gmx_mpi solvate -cp min_dopc.gro -cs spc216.gro -o solvate.gro -p

Re: [gmx-users] Implicit Solvent and Box Size

On 10/7/19 11:12 AM, zhangzhu...@hotmail.com wrote: Dear Paul, Thanks for your advice. Since my system is acidic, I thought implicit solvent would get better approximation as I read from the GROMACS website. So there was no idea about my problem? Implicit solvent is used without PBC and

[gmx-users] Shape of the aggregate

Hi I am trying to calculate the shape of an aggregate which is cylindrical in shape. I have used the command gmx polystat -f aggregate.pdb -s aggregate.tpr -o poly.xvg The eigen values from gmx polystat of the aggregate for a particular frame are 3.3566 0.8837 0.7660 but using VMD the

Re: [gmx-users] Implicit Solvent and Box Size

Dear Paul, Thanks for your advice. Since my system is acidic, I thought implicit solvent would get better approximation as I read from the GROMACS website. So there was no idea about my problem? Thanks! Zhuo -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Implicit Solvent and Box Size

Hi, I am doing the aggregations of small peptides in implicit solvents. However, it seems that there is no detailed tutorial on such subject and I just turned on the 'implicit solvent' option in the .mdp file. However, I found that the box was compressed during mdrun. It comes to me that the

Re: [gmx-users] Implicit Solvent and Box Size

Hello, the implicit solvent functionality has been deprecated a while ago in GROMACS and has been removed in the recent versions. Can the simulations also be run in explicit solvents (that are a better physical representation anyway)? Cheers Paul On 07/10/2019 16:50, 张 卓 wrote: Hi, I am

[gmx-users] Implicit Solvent and Box Size

Hi, I am doing the aggregations of small peptides in implicit solvents. However, it seems that there is no detailed tutorial on such subject and I just turned on the 'implicit solvent' option in the .mdp file. However, I found that the box was compressed during mdrun. It comes to me that the

Re: [gmx-users] Gromacs2019 + Gaussian09 QMMM (nikol...@spbau.ru)

Hi Good point. The environment variable names changed. Thus $GMX_QM_MODIFIED_LINKS_DIR is what used to be DEVIL_DIR The same for the others. Gerrit > Good 4. Re: Gromacs2019 + Gaussian09 QMMM (nikol...@spbau.ru) > > > Dear Gerrit, > > Thank you very much for your answer. > As I

[gmx-users] Solvation of protein on membrane surface

Dear all, I would like to perform a simulation of protein on a membrane surface. Following the placement of the protein on the DOPC surface I solvated the system by the following command: gmx_mpi solvate -cp min_dopc.gro -cs spc216.gro -o solvate.gro -p system.top I made a local copy of

Re: [gmx-users] Simulation of membrane associated protein

Thank you! *Olga Press-Sandler* Ph.D. student, Yifat Miller's lab Department of Chemistry Ben-Gurion University, Israel -- 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] Solvation of protein on membrane surface .JPG

I've shared an item with you: Solvation of protein on membrane surface .JPG https://drive.google.com/file/d/1cdYTCn7PLrRrt4aUSHz40WTLG7QZ9xzP/view?usp=sharing=5d9ae82d It's not an attachment -- it's stored online. To open this item, just click the link above. Dear all, I would like to