Re: [gmx-users] Exclusions in topology file seem not working for big systems

so it seems that I don't need to use exclusions anymore. Regards, Reza Salari From: Berk Hess To: Discussion list for GROMACS users Sent: Fri, December 4, 2009 8:01:34 AM Subject: RE: [gmx-users] Exclusions in topology file seem not working for big sy

RE: [gmx-users] Exclusions in topology file seem not working for big systems

not. Berk Date: Thu, 3 Dec 2009 10:40:08 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org Thank you very much Dr Hess. Then I guess I have to test my rerun workaround that I mentioned for my system.

Re: [gmx-users] Exclusions in topology file seem not working for big systems

, 2009 12:06:53 PM Subject: RE: [gmx-users] Exclusions in topology file seem not working for big systems Hi, I think that for your problem the couple option is not useful. It does exactly the opposite. I removes all interactions of the selected molecule type with the rest of the system and

RE: [gmx-users] Exclusions in topology file seem not working for big systems

ns. (which end up in special 1-4 energy terms). Berk Date: Thu, 3 Dec 2009 08:59:12 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org Thanks Dr Hess. I didn't get an error message when using gromp

Re: [gmx-users] Exclusions in topology file seem not working for big systems

3, 2009 3:30:27 AM Subject: RE: [gmx-users] Exclusions in topology file seem not working for big systems Hi, If you really had too many exclusions you would get an error message. So I just tested this. I used the couple_moltype option to couple a 389 atom protein. This generates exclusions betwe

RE: [gmx-users] Exclusions in topology file seem not working for big systems

special 1-4's because of the couple option). So I don't understand what is going wrong in your case. Berk Date: Wed, 2 Dec 2009 09:31:03 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org Thank

Re: [gmx-users] Exclusions in topology file seem not working for big systems

. Regards, Reza Salari From: David van der Spoel To: Discussion list for GROMACS users Sent: Wed, December 2, 2009 11:59:49 AM Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems Reza Salari wrote: > Hi All, > > I seem

Re: [gmx-users] Exclusions in topology file seem not working for big systems

Reza Salari wrote: Hi All, I seem to have a hard time to use exclusions in topology file. I have a relatively big system (~400 aa) that I am trying to calculate the difference in desolvation energy (dA) upon turning off charges on a specific residue using thermodynamics integration method. Th