[gmx-users] Re: [gmx-developers] low concentration simulation ?

Chih-Ying Lin wrote: HI I am simulating the protein + ligand + water molecules system. In the experimental work, the concentration of ligand is pretty low, say under 20 mM (avearge 18 ligands attached on one protein) It will be a huge system to create a system with 20 mM and it will take

Re: [gmx-users] trouble minimizing structure with mdrun

maybe I should go directly from pdb2gmx to grompp seeing as I have already solvated and ionized the protein in VMD. On Mon, Jan 4, 2010 at 8:04 PM, Jack Shultz wrote: > I did a little more checking on the structures, I notice the results > from genion move part of the protein far outside the sol

Re: [gmx-users] trouble minimizing structure with mdrun

I did a little more checking on the structures, I notice the results from genion move part of the protein far outside the solvent box. I shall try this without the genion step I put all the files in the working directory for this preperation in a zip archive under http://boinc.drugdiscoveryathome.

RE: [gmx-users] Fwd: What could be wrong with rdf plot?

Wouldn't it be simpler to just exclude the intramolecular -OHs when you actually generate the RDF? Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx

[gmx-users] Simulation Box break into 16 domains => .tpr file is wrong (Gromacs 3.3.3)

Hi, Thanks a lot, Tsjerk ! My simulation is running. I never knew that a discrepancy between the the .top file and .gro, grompp uses the topology information in stead of the coordinate file information. What does issue a set of warnings by grompp ? How do you know the discrepancy between the th

Re: [gmx-users] Fwd: What could be wrong with rdf plot?

It is always better to keep the discussion in the list. Someone could benefit of it as well as you from others. From: Lum Nforbi Date: January 4, 2010 7:57:04 PM GMT+01:00 To: XAvier Periole Subject: Thank you for reply on RDF PLOT problem/Question. Hi Xavier, Is there something I can do in

Re: [gmx-users] trouble minimizing structure with mdrun

Hi Jack, > On Mon, Jan 4, 2010 at 2:44 AM, Tsjerk Wassenaar wrote: >> Hi Jack, >> >> After preparation with (V|NA)MD, did pdb2gmx correctly assign chains, >> or did it tie chains together? In the latter case it would have issued >> a number of "Long Bond Warnings". Did anything else odd show u

[gmx-users] Calculation of Cp

Dear All, I have been struggling with this for over a month now and I have still not been able to figure out how to calculate the Cp of my system of 2000 molecules of water on which I did an NPT simulation. The g_energy command of my system gives a wrong Cv (~12.4749 J/mol.K), which therefore

Re: [gmx-users] Fwd: mdrun error

Amir Marcovitz wrote: -- Forwarded message -- From: *Amir Marcovitz* mailto:amarcov...@gmail.com>> Date: Mon, Jan 4, 2010 at 6:18 PM Subject: mdrun error To: gmx-users-requ...@gromacs.org Hi, my system is composed of 2 molecules that

[gmx-users] Fwd: mdrun error

-- Forwarded message -- From: Amir Marcovitz Date: Mon, Jan 4, 2010 at 6:18 PM Subject: mdrun error To: gmx-users-requ...@gromacs.org Hi, my system is composed of 2 molecules that are arranged in a lattice: i.e., each molecule is represented by 4 atoms (which are charged) and o

Re: [gmx-users] Dead Link or Restricted Access to link

Thanks! On Mon, Jan 4, 2010 at 5:13 AM, zjxu wrote: > Jack Shultz 写道: > > The links to the videos don't work on this page. > Hybrid QM/MM simulations with GROMACS, QM/MM application (slides,video > 1,video 2,video 3) - (Gerrit Groenhof). > http://www.gromacs.org/Documentation/How-tos/QMMM > > > H

Re: [gmx-users] trouble minimizing structure with mdrun

It seemed to run in NAMD with or without the infamous Fe4S4 center gromacs with amber99SB or OPLSA with or without exotic species seems to fail. Eventually I want to figure out this QM/MM integration with MOPAC but that is a subject for later. Let me at least see if pure MM works. I noticed that th

Re: [gmx-users] Problems with g_hbond

Rolf Erwin Isele-Holder wrote: Dear users, I'm running a simulation which uses ethanol as solvent. When using g_hbond the programm is able to recognize the solute's donors and acceptors, however it does not recognize any acceptors or donors of ethanol. Here is a part of my topology: [ atoms

Re: [gmx-users] grompp segmentation error

ram bio wrote: Dear Justin, Thanks for the response. I am using gromacs 4.0.3 version on my PC and 4.0.5 on cluster, I have asked my system admin to provide the details regarding the cluster, whereas for my PC: The info is as follows: 1. The Gromacs version you are using. - 4.0.3 2. The com

Re: [gmx-users] grompp segmentation error

Dear Justin, Thanks for the response. I am using gromacs 4.0.3 version on my PC and 4.0.5 on cluster, I have asked my system admin to provide the details regarding the cluster, whereas for my PC: The info is as follows: 1. The Gromacs version you are using. - 4.0.3 2. The compilers used in inst

Re: [gmx-users] Problems with g_hbond

Hi Rolf, Try renaming the atom names to something that starts with O and H for oxygen and hydrogen. Good luck, Ran. Rolf Erwin Isele-Holder wrote: > Dear users, > > I'm running a simulation which uses ethanol as solvent. When using g_hbond > the programm is able to recognize the solute's donors a

[gmx-users] Problems with g_hbond

Dear users, I'm running a simulation which uses ethanol as solvent. When using g_hbond the programm is able to recognize the solute's donors and acceptors, however it does not recognize any acceptors or donors of ethanol. Here is a part of my topology: [ atoms ] ; nr type resnr residu

[gmx-users] Re: a question about gromacs-water tutorial

Please keep all Gromacs-related correspondence on the gmx-users list. This has nothing to do with any of my tutorials, and as such, is better posted to the community. As I seem to post every other day or so, I am not a private tutor or help service. The grompp.mdp file in the /share/tutor

Re: [gmx-users] Dead Link or Restricted Access to link

Jack Shultz ??: The links to the videos don't work on this page. Hybrid QM/MM simulations with GROMACS, QM/MM application (slides,video 1,video 2,video 3) - (Gerrit Groenhof). http://www.gromacs.org/Documentation/How-tos/QMMM Hi Jack, I will send this message to the one who is in charge of t