Re: [gmx-users] Free energy of transfer with accuracy

Chris, Also, if your C60 is hollow, I can imagine that it might exclude solvent atoms from the inside, in which case you are going to have a big convergence issue as solvent begins to interpenetrate with the C60, which may lead to noise problems when this starts to happen, whatever soft core

Re: [gmx-users] Free energy of transfer with accuracy

Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ Subject: Re: [gmx-users] Free energy of transfer with accuracy

Re: [gmx-users] Free energy of transfer with accuracy

Hi, Hi gmx-users, I have tried to calculate the free energy of transfer of a solute between two solvents by thermodynamic integration. However, the dgdl plot I have obtained is not smooth enough to ensure accuracy. I have used a non homogeneous spacing for lambda. The first is from 0.0 to

Re: [gmx-users] Free energy of transfer with accuracy

André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ -- Message: 4 Date: Thu, 11 Dec 2008 07:24:26 -0600 From: David Mobley [EMAIL PROTECTED] Subject: Re: [gmx-users] Free energy of transfer with accuracy To: Discussion list

Re: [gmx-users] Free energy of transfer with accuracy

, 11 Dec 2008 07:24:26 -0600 From: David Mobley [EMAIL PROTECTED] Subject: Re: [gmx-users] Free energy of transfer with accuracy To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Hi, Hi gmx-users

[gmx-users] Free energy of transfer with accuracy

Hi David, I found this comment quite interesting: Also, if your C60 is hollow, I can imagine that it might exclude solvent atoms from the inside, in which case you are going to have a big convergence issue as solvent begins to interpenetrate with the C60, which may lead to noise problems when

Re: [gmx-users] Free energy of transfer with accuracy

, 166 - Bloco B, Sala 1048 09210-170 Santo André - SP Brasil +55.11.4437-8408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ Subject: Re: [gmx-users] Free energy of transfer with accuracy To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED

[gmx-users] Free energy of transfer with accuracy

Hi gmx-users, I have tried to calculate the free energy of transfer of a solute between two solvents by thermodynamic integration. However, the dgdl plot I have obtained is not smooth enough to ensure accuracy. I have used a non homogeneous spacing for lambda. The first is from 0.0 to 0.4