[gmx-users] 1-4 interactions free energy calculations

Hi all! I have been running a series of simulations for coupling a molecule (free energy calculations). All my settings and parameters in the mdp file worked great for one system, but then I change the molecule to a bigger one and I started to have warnings about 1-4 interactions: Warning: 1-4

Re: [gmx-users] 1-4 interactions free energy calculations

On 6/24/13 1:07 PM, Sonia Aguilera wrote: Hi all! I have been running a series of simulations for coupling a molecule (free energy calculations). All my settings and parameters in the mdp file worked great for one system, but then I change the molecule to a bigger one and I started to have

[gmx-users] 1-4 interactions warning

Hi, I am using gromacs 4.5 and i am trying to run an energy minimization and then temperature equilibration for a system of two charged plates plates solvented in water. the plates are made of fake atoms which has carbon atoms parameters, and a bond length of 0.2 nm. the plates are made from

Re: [gmx-users] 1-4 interactions warning

On Wed, Apr 10, 2013 at 9:51 AM, Liron Cohen liron.co...@weizmann.ac.ilwrote: Hi, I am using gromacs 4.5 and i am trying to run an energy minimization and then temperature equilibration for a system of two charged plates plates solvented in water. the plates are made of fake atoms which has

[gmx-users] 1-4 interactions

After reading the manual and trying to find more information on the mailing list. I'm still not sure about this 1-4 interactions, when I want to calculate the energy between two groups (lets say one residue and the rest of the protein) should I sum everything (including the 1-4 interactions) or

Re: [gmx-users] 1-4 interactions

On 4/3/13 7:16 AM, Liron Cohen wrote: After reading the manual and trying to find more information on the mailing list. I'm still not sure about this 1-4 interactions, when I want to calculate the energy between two groups (lets say one residue and the rest of the protein) should I sum

RE: [gmx-users] 1-4 interactions

users Subject: Re: [gmx-users] 1-4 interactions On 4/3/13 7:16 AM, Liron Cohen wrote: After reading the manual and trying to find more information on the mailing list. I'm still not sure about this 1-4 interactions, when I want to calculate the energy between two groups (lets say one residue

Re: [gmx-users] 1-4 interactions

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Wednesday, April 03, 2013 2:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] 1-4 interactions On 4/3/13 7:16 AM

Re: [gmx-users] 1-4 interactions

You can either specify this explicitly or use the fudge LJ and fudge q headers in your topology file. See the manual for details. On Sep 26, 2009, at 1:51 AM, Vitaly V. Chaban wrote: Hi, Is it possible in gromacs to make 1-4 interaction energy reduced as compared to the intermolecular

[gmx-users] 1-4 interactions

Hi, Is it possible in gromacs to make 1-4 interaction energy reduced as compared to the intermolecular interations between the same centers? In other words, I want the INTRAmolecular interaction A-B to be by some factor smaller than INTERmolecular A-B interactions in the box. Thanks, Vitaly

Re: [gmx-users] 1-4 Interactions

Hi, Thanks for the prompt responses. I checked the distance between atoms 908 and 913 in VMD and got 0.396nm, which seems fine. I thought then, that my problem may be with my box size when I used editconf. When I changed the box dimension to 2.0nm from the molecule periphery, the warning

Re: [gmx-users] 1-4 Interactions

toma0052 wrote: Hi, Thanks for the prompt responses. I checked the distance between atoms 908 and 913 in VMD and got 0.396nm, which seems fine. I thought then, that my problem may be with my box size when I used editconf. When I changed the box dimension to 2.0nm from the molecule

Re: [gmx-users] 1-4 Interactions

toma0052 wrote: Hello, I am starting simulations on a DPPC lipid bilayer taken from Peter Tieleman's website. Upon trying to run the energy minimization, the program runs, but the results does not appear correct. During the run, I get the warning: Warning: 1-4 interaction between 908 and