On 3/1/16 7:59 PM, Khuong Truong Gia wrote:
Hi all,
I am using gromacs to run umbrella sampling simulation with a drug molecule
(polymer). I got force field from PRODRG.
When run pulling the drug I got this error:
step 86530014: Water molecule starting at atom 8336 can not be settled.
Check
Hi all,
I am using gromacs to run umbrella sampling simulation with a drug molecule
(polymer). I got force field from PRODRG.
When run pulling the drug I got this error:
step 86530014: Water molecule starting at atom 8336 can not be settled.
Check for bad contacts and/or reduce the timestep if
Dear all,
im running umbrella sampling when invoke the following command i got the
follwoing warnings and grompp terminated becasue of so much warning
,initially i neutralised the My protein-Ligand system with NACl,so how come
there will be a charge? (NOTE 5)what i can do for that? can i use
On 1/5/16 5:36 AM, Nikhil Maroli wrote:
Dear all,
im running umbrella sampling when invoke the following command i got the
follwoing warnings and grompp terminated becasue of so much warning
,initially i neutralised the My protein-Ligand system with NACl,so how come
there will be a charge?
On 4/23/15 10:34 AM, Jianhui Tian wrote:
Date: Wed, 22 Apr 2015 19:23:32 -0400
From: Justin Lemkul jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling Error in Gromacs 5.0
Message-ID: 55382d74.5070...@vt.edu
Content-Type: text/plain; charset=windows-1252
Dear Users,
I am trying to do a umbrella pulling of one lipid out of a bilayer using
umbrella sampling code. In Gromacs 5.0, there is a big change in umbrella
sampling implementation. I set my pull parameters like this:
pull = umbrella
pull_geometry = cylinder ; Pull in the
Date: Wed, 22 Apr 2015 16:05:18 -0400
From: Justin Lemkul jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling Error in Gromacs 5.0
Message-ID: 5537fefe.6020...@vt.edu
Content-Type: text/plain; charset=windows-1252; format=flowed
On 4/22/15 3:54 PM
On 4/22/15 3:54 PM, Jianhui Tian wrote:
Dear Users,
I am trying to do a umbrella pulling of one lipid out of a bilayer using
umbrella sampling code. In Gromacs 5.0, there is a big change in umbrella
sampling implementation. I set my pull parameters like this:
pull = umbrella
