behalf of Lukas
Zimmermann <luk.zi...@gmail.com>
Sent: 20 June 2016 06:03:51
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] PMF steadily increasing
Thank you again for your remarks. This is what I found so far:
(1) With gmx mindist it was very clear that protein and peptide do not
interact. Fo
mes unbound and can
>> then sample full X and Y, but on its own that should not continue to impact
>> the sampling after contact is permanently broken.
>>
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sy
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Lukas
> Zimmermann <luk.zi...@gmail.com>
> Sent: 15 June 2016 12:45:51
> To: gmx-us...@gromacs.org
> Subject
is permanently broken.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Lukas
Zimmermann <luk.zi...@gmail.com>
Sent: 15 June 2016 12:45:51
To: gmx-us...@gromacs.org
Subject: [gmx-users]
Dear GROMACS community,
I performed umbrella sampling study to estimate the binding free energy
between a globular
protein with 568 residues and a small peptide with 13 residues. I use the
pull code with k = 800 and rate = 0.005 to generate the initial
conformations over the time course of 1200
