Dear gmx users,
I am using gmx wham to analyse umbrella sampling simulations. I have 30
positions along the reaction coordinate and therefore 30 tpr, pullf and pullx
files. Each of these files have 100,000 rows, as I save every ps.
When I try to execute wham with the command:
gmx wham -it
constrain command.
Thank you once again for your time.
Kind Regards,
Michail
On 03/02/16 22:05, Szilárd Páll wrote:
> --
> Szilárd
>
>
> On Tue, Feb 2, 2016 at 3:34 PM, Michail Palaiokostas Avramidis
> <m.palaiokos...@qmul.ac.uk> wrote:
>>
>> On 02/02/16 14:04, S
On 02/02/16 14:04, Szilárd Páll wrote:
> On Tue, Feb 2, 2016 at 11:17 AM, Michail Palaiokostas Avramidis
> <m.palaiokos...@qmul.ac.uk> wrote:
>> Hi Mark and thank you for your answer.
>> Please see below :)
>>
>> On 01/02/16 18:28, Mark Abraham wrote:
>>
Hi Mark and thank you for your answer.
Please see below :)
On 01/02/16 18:28, Mark Abraham wrote:
> Hi,
>
> On Mon, Feb 1, 2016 at 6:42 PM Michail Palaiokostas Avramidis <
> m.palaiokos...@qmul.ac.uk> wrote:
>
>> Dear GMX users,
>>
>>
>> I wou
Dear GMX users,
I would like to ask about your opinion on the size of the neighbour list
(nstlist).
I am running constraint simulations of a permeant along a lipid bilayer. In the
initial setup the system runs on NPT and nstlist 10 (which GROMACS changes to
40 automatically). With this
Tuesday, January 19, 2016 9:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] GROMACS performance with an NVidia Tesla k40c
Hi,
On Tue, Jan 19, 2016 at 8:34 PM, Michail Palaiokostas Avramidis <
m.palaiokos...@qmul.ac.uk> wrote:
> Dear GMX users,
>
>
> I have recent
Dear GMX users,
I have recently installed an Nvidia Tesla K40c in my workstation (already had a
quadro k2000) and I am currently trying to optimize its usage with GROMACS. I
used two compilations of GROMACS, one is the standard one as suggested in the
beginning of the installation
On 11/01/16 21:48, Justin Lemkul wrote:
>
>
> On 1/11/16 3:39 PM, Michail Palaiokostas Avramidis wrote:
>> Dear GMX users,
>>
>>
>> I am currently facing some stability issues when using the com
>> pulling to constrain the distance between two gr
Dear GMX users,
I am currently facing some stability issues when using the com pulling to
constrain the distance between two groups and I would appreciate any help on
the issue.
I am trying to simulate a lipid bilayer with a small molecule introduced at
several positions along the z-axis
