concentrations are small.]
So there is no concentration term to consider.
Warren Gallin
> On Mar 1, 2015, at 2:27 PM, Alexander Law
> wrote:
>
> Dear gmx-users
>
> Is it possible to produce a valid dissociation constant value from gibbs free
> energy value produced from umbrella sampl
Dear gmx-users
Is it possible to produce a valid dissociation constant value from gibbs free
energy value produced from umbrella sampling?
The equation is given at the bottom of the this wikipedia page:
http://en.wikipedia.org/wiki/Binding_constant
Is the concentration term vital since the lig
Error in equation, see the equation at the bottom of this wiki page:
http://en.wikipedia.org/wiki/Binding_constant
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Alexander Law
Is it possible to use the Gibbs free energy value produced from an umbrella
sampling experiment to calculate the dissociation constant?
The PMF difference between the energy minimum to the plateau region is -18 kcal
mol-1 what is the Kd value?
Is the following equation applicable?:
Kd =e^(***
Add: "-cpi state.cpt" to your command line. And change your .mpd file to
reflect the time you want to use.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Abid Channa
[abid.cha...@ho
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul
[jalem...@vt.edu]
Sent: Friday, February 06, 2015 12:07 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Samling Alteration
On 2/4/15 7:22 PM, Alexander Law
-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul
[jalem...@vt.edu]
Sent: Tuesday, February 03, 2015 1:51 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Samling Alteration
On 2/1/15 11:22 PM, Alexander Law wrote:
> D
Dear Gromacs Users
I am currently running the series of simulations using the following command:
mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
I wish to lessen the amount of time for each of these simulations from 10 ns to
6 ns. These simulations are already up to arou
Dear Gromacs Users
I have been running umbrella sampling, during Step Six: Umbrella Sampling
Simulations, using the code:
mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
my simulation crashed and I wish to continue it using the -cpi umbrella0.cpt
method but 2 .cpt files
Dear gmx-users
I am running umbrella sampling and running the last simulations before analysis
using this command:
mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
Some of my simulations have crashed before completion and I wish to continue
them, in the past I have used
Ignore message, didn't read correctly
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of soumadwip
ghosh [soumadwipgh...@gmail.com]
Sent: Thursday, December 04, 2014 7:25 PM
To: gromacs.
Hey
You may benefit from the make_ndx command. This allows to make a custom index
group and you can add individual atoms as 1 group with only one element.
http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx
Also, I recommend you decide on a time cut off points using -b (start) -e (e
This error occurs because the shortest distance will be used for analysis.
There are 2 distances, the linear distance between group 0 and group 1, the
other distance passes outside the PBC and enters on the otherside, at the
backside of group0. Your box is too small, increase the distance of the
-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul
[jalem...@vt.edu]
Sent: Monday, November 24, 2014 1:47 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling gromacs 5.0 error
On 11/23/14 3:56 PM, Alexander Law wrote:
> Hi Justin
>
> I downloaded the compressed fo
Re: [gmx-users] Umbrella Sampling gromacs 5.0 error
On 11/21/14 7:26 AM, Justin Lemkul wrote:
>
>
> On 11/20/14 7:52 PM, Alexander Law wrote:
>> Hi Justin
>>
>> Thank you for taking the time and helping me out. I am now using the 4.6.5
>> version to avoid this sort of
: Wednesday, November 19, 2014 1:28 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling gromacs 5.0 error
On 11/17/14 11:02 PM, Alexander Law wrote:
> Dear vmx-users
>
> I am running through Dr Lemkul's umbrella sampling tutorial and applying this
> to my own
Dear vmx-users
I am running through Dr Lemkul's umbrella sampling tutorial and applying this
to my own structure. I have problem with the pull simulation command: grompp -f
md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr
I receive this error message back:
Ignoring obso
You need to investigate further for your particular system and the questions
you want answered. Then come back with specific questions and problems.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se
I may have found a bug in the vmx hbond command. In short the cyclic nitrogen
within the indole ring on a tryptophan side chain is behaving as both Hbond
acceptor and donor. The end result of this is a constant Hbond being show in
the output .xvg. Here are some of the detail which led me to this
alexander@pg.canterbury.ac.nz
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