[gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

ergy wells present at the edge of the hydrogen terminated graphene sheet. Just looking for your comments and thoughts. Thanks. Darrell Date: Sun, 01 Nov 2009 18:20:26 +1100 From: Mark Abraham Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa To: Discussion list for GRO

Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

stin's right inasmuch as amide N-H type 241 has no H LJ parameters. Perhaps there's other text that Darrell hasn't found yet, or backbone nitrogen is not considered a heteroatom :-). Mark Darrell Date: Mon, 19 Oct 2009 19:07:22 +1100 From: Mark Abraham Subject: R

[gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

atoms? Thanks. Darrell Date: Mon, 26 Oct 2009 08:47:14 +1100 From: Mark Abraham Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa To: Discussion list for GROMACS users Message-ID: <4ae4c762.2060...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1;

Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

arrell Date: Mon, 19 Oct 2009 19:07:22 +1100 From: Mark Abraham Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa To: Discussion list for GROMACS users Message-ID: <4adc1e3a.8010...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskin

Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

, all N-H bonds involved hydrogen atoms with zero LJ parameters. See, for example, any backbone NH, amide (ASN/GLN), or amine (LYS/LYSH), etc and you will see the atom types used. -Justin Thanks. Darrell Date: Mon, 19 Oct 2009 19:07:22 +1100 From: Mark Abraham Subject: Re: [gmx-users] Lennard

[gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

s ", it appears to me that a site for a non-bonded interaction should exist on the H atoms within ammonia. Is my interpretation incorrect? Thanks. Darrell Date: Mon, 19 Oct 2009 19:07:22 +1100 From: Mark Abraham Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffopls

Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

Darrell Koskinen wrote: Hi, I see that the Lennard Jones parameters for the N & H atoms in ammonia, represented by opls_127 and opls_128 in the file ffoplsaanb.itp are: opls_127 NT 7 14.00670-1.020 A3.42000e-01 7.11280e-01 opls_128 H 1 1.00800 0.340 A

[gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

Hi, I see that the Lennard Jones parameters for the N & H atoms in ammonia, represented by opls_127 and opls_128 in the file ffoplsaanb.itp are: opls_127 NT 7 14.00670-1.020 A3.42000e-01 7.11280e-01 opls_128 H 1 1.00800 0.340 A0.0e+00 0.0e