[gmx-users] measuring surface tension

Dear gmx users, Is it possible to measure surface tension with time in a protein adsorption process at oil-water interface in Gromacs? if yes how, any help is highly appreciated. Cheers David -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Details about using g_wham

Unless you symmetrize the PMF before output, it should be along an entire box side. You do not specify how you pulled your molecule; therefore, it is impossible to suggest further. Dr. Vitaly V. Chaban Виталий Витальевич ЧАБАН On Tue, Jul 29, 2014 at 1:42 AM, Yoo Chan Myung

Re: [gmx-users] Some columns in log file.

On 7/28/14, 10:11 PM, Theodore Si wrote: For example, a form that explains the meanings of the all items in the log file. I found this page

Re: [gmx-users] hints for core/shell optimization?

Dear Justin, I've tried applying the [thole_polarization] section in the format you've suggested. I've noticed the followings. 1. First I made a mistake and forgot to remove the [polarization] section from the TOP file. Even this way MDRUN worked and indicated the usual ca. 10 kJ/mol

[gmx-users] !Help!: Normal Mode Analysis

Dear all, I wonder if there is anywhere I can know the details of mdp files used for normal mode analysis. I understand from the maunal that it needs steepest descent, conjugate gradient, l-bfgs, nm in md options consecutively, but I am not sure about other parameters set in these

Re: [gmx-users] !Help!: Normal Mode Analysis

Hi, I am not an expert, but I think there is no such tricky parameter for normal mode calculation though I don't know what your situation is.. You can find some tips at the below link.. http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis If you set parameters extremely wrong the

[gmx-users] No default Proper Dih. types

Hi, I'm attempting to simulate polyethylene using OPLS. I'm using the files from: https://www.mail-archive.com/gmx-users@gromacs.org/msg19683.html I can process gencofig these files, however when I try to grompp, I get the error: ERROR 1 [file topol.top, line 162]: No default Proper Dih.

[gmx-users] Grompp not finding proper dihedral

Hi, I'm attempting to simulate polyethylene using OPLS (I'm using Gromacs 5.0.1-dev). I'm using the files from: https://www.mail-archive.com/gmx-users@gromacs.org/msg19683.html I have moved the OPLS force field directory to my working directory and placed ffoplsaa.rtp and ffoplsaa.hdb in the

Re: [gmx-users] hints for core/shell optimization?

On 7/29/14, 9:33 AM, Tamas Karpati wrote: Dear Justin, I've tried applying the [thole_polarization] section in the format you've suggested. I've noticed the followings. 1. First I made a mistake and forgot to remove the [polarization] section from the TOP file. Even this way MDRUN worked

Re: [gmx-users] Grompp not finding proper dihedral

On 7/29/14, 2:45 PM, John Doe wrote: Hi, I'm attempting to simulate polyethylene using OPLS (I'm using Gromacs 5.0.1-dev). I'm using the files from: https://www.mail-archive.com/gmx-users@gromacs.org/msg19683.html I have moved the OPLS force field directory to my working directory and

[gmx-users] Molecular solid NPT simulation problem

Dear Gromacs users, I'm currently working with organic molecular solids and I'm trying to follow the protocol stablished in JCP, 139, 034104 (2013) (DOI: 10.1063/1.4812362). Before a production run in the NVT ensemble to get the Helmholtz potential for a certain molecular solid, I have to get the

Re: [gmx-users] Some columns in log file.

thnks a lot ! 于2014年7月29日 19:53:19,Justin Lemkul写到: On 7/28/14, 10:11 PM, Theodore Si wrote: For example, a form that explains the meanings of the all items in the log file. I found this page

[gmx-users] POPC/POPC structures

Dear Gmx Users, Would someone suggest where I could find strucutre of POPC and POPS lipids which once processed by pdb2gmx and Charmm36 would provide me a topology? I found many stuctures but atoms are not matching and i have no clue which one in the structure coresponds to which one in pdb.

Re: [gmx-users] POPC/POPC structures

http://wcm.ucalgary.ca/tieleman/downloads you can make the topology by command pdb2gmx On Wed, Jul 30, 2014 at 8:23 AM, Steven Neumann s.neuman...@gmail.com wrote: Dear Gmx Users, Would someone suggest where I could find strucutre of POPC and POPS lipids which once processed by pdb2gmx and

Re: [gmx-users] POPC/POPC structures

Thanks a lot! How about POPS? On Wed, Jul 30, 2014 at 12:26 PM, RINU KHATTRI nickname.mi...@gmail.com wrote: http://wcm.ucalgary.ca/tieleman/downloads you can make the topology by command pdb2gmx On Wed, Jul 30, 2014 at 8:23 AM, Steven Neumann s.neuman...@gmail.com wrote: Dear Gmx