RE: [gmx-users] set charge as 0 in gromacs code

2013-08-07 Thread Mark Abraham
t; > Stony > > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on > behalf of Mark Abraham [mark.j.abra...@gmail.com] > Sent: Tuesday, August 06, 2013 8:20 PM > To: Discussion list for GROMACS users > Subject: Re: [gm

RE: [gmx-users] set charge as 0 in gromacs code

2013-08-06 Thread Shi, Yu (shiy4)
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.j.abra...@gmail.com] Sent: Tuesday, August 06, 2013 8:20 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] set charge as 0 in gromacs code Ewald self

Re: [gmx-users] set charge as 0 in gromacs code

2013-08-06 Thread Mark Abraham
Ewald self energy, perhaps? Mark On Wed, Aug 7, 2013 at 1:16 AM, Shi, Yu (shiy4) wrote: > Hello everyone, > > My system is 512 waters and 1 ion CL-. Now I would like to change the CL > charge as 0 in the gromacs code for the short non-bonded interaction. While > for the long-range electrosta

[gmx-users] set charge as 0 in gromacs code

2013-08-06 Thread Shi, Yu (shiy4)
Hello everyone, My system is 512 waters and 1 ion CL-. Now I would like to change the CL charge as 0 in the gromacs code for the short non-bonded interaction. While for the long-range electrostatics (pme) the CL is -1. My gromacs version is 4.6.2, which automatically starts 8 threads to com