Hi Friends,
How to get a "graph of potential as function of time" ?? Currently I am
using gmx potential script to generate potential.xvg but it is showing
potential as function of boxlength.
reg
Rituraj
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Thank you Mark sir.
On Mon, Jan 21, 2019, 8:27 AM Mark Abraham Hi,
>
> I suggest you don't ask for "within 0.5 of com of protein" if what you want
> is e.g. "within 0.5 of protein"
>
> Mark
>
> On Mon, Jan 21, 2019 at 3:51 AM ISHRAT JAHAN wrote:
>
> > Thanks for the reply Justin sir.Please tell
I have calculated it and from there i got the forst hydration layer.
On Mon, Jan 21, 2019, 8:29 AM Bratin Kumar Das <177cy500.bra...@nitk.edu.in
wrote:
> Calculate the rdf first
>
> On Mon 21 Jan, 2019, 8:22 AM ISHRAT JAHAN
> > Thanks for the reply Justin sir.Please tell me the right command as
Calculate the rdf first
On Mon 21 Jan, 2019, 8:22 AM ISHRAT JAHAN Thanks for the reply Justin sir.Please tell me the right command as i have
> to calculate it from the surface of protein.
>
> On Mon, Jan 21, 2019, 1:39 AM Justin Lemkul
> >
> >
> > On 1/20/19 1:01 AM, ISHRAT JAHAN wrote:
> > >
Hi,
I suggest you don't ask for "within 0.5 of com of protein" if what you want
is e.g. "within 0.5 of protein"
Mark
On Mon, Jan 21, 2019 at 3:51 AM ISHRAT JAHAN wrote:
> Thanks for the reply Justin sir.Please tell me the right command as i have
> to calculate it from the surface of protein.
Thanks for the reply Justin sir.Please tell me the right command as i have
to calculate it from the surface of protein.
On Mon, Jan 21, 2019, 1:39 AM Justin Lemkul
>
> On 1/20/19 1:01 AM, ISHRAT JAHAN wrote:
> > Dear all,
> > I want to calculate the number of water molecule within 5 A of protein
On 1/20/19 7:48 PM, Lianxin Xin wrote:
Hi, everyone,
I am running a GROMACS (V5.1.2) simulation of GOLD interacting with
protein. I am looking for CHARMM26 force field, can anyone send me the
link to download the force field?
This is not a question related to GROMACS development, so
Hi,
The hard-coded SOL reference that Justin mentioned has been fixed in Gromacs
2018.3 and 2019. If you upgrade your gromacs version, gmx solvate should work
as intended.
Kevin
> On Jan 20, 2019, at 3:11 PM, Justin Lemkul wrote:
>
>
>
>> On 1/20/19 3:04 PM, ZHANG Cheng wrote:
>> In the
Hi,
They're inactive so whether they have any value or are present does not
matter.
Mark
On Sun., 20 Jan. 2019, 10:34 Olga Press, wrote:
> Dr. Mark Abraham, thank you so much for your help.
> That meaning that in the NPT equilibration without position restrains
> the refcoord_scaling should
On 1/20/19 3:04 PM, ZHANG Cheng wrote:
In the command
gmx solvate -cp 128_minimized.gro -cs water.gro -o waterbox.gro -maxsol 768
-radius 0.21 -p dppc.top
768 waters are added, resulting in the "waterbox.gro".
However, the "dppc.top" is not updated for its "[ molecules ]" section. I
On 1/20/19 8:56 AM, Quin K wrote:
I can dual boot windows and Ubuntu on my computer but since I'm doing
docking with AutoDock I'm using windows.
AutoDock can be installed easily on Linux.
What is your opinion should I use Ubuntu or Windows 10 for Gromacs MD
simulations?
Will I face
On 1/20/19 1:01 AM, ISHRAT JAHAN wrote:
Dear all,
I want to calculate the number of water molecule within 5 A of protein
throughout the trajectory. I have calculated it using the command-
gmx select -n water.ndx -select 'group "water" and within 0.5 of com of
group "Protein" -os out.xvg
On 1/18/19 11:55 AM, marzieh gharouni wrote:
Hello
I did a simulation of protein-protein interaction with Gromacs code. In
this simulation, the number of amino acids in each protein is about 230.
The simulation production run was 300ns. After analyzing trajectory, I
found that RMSD value of
In the command
gmx solvate -cp 128_minimized.gro -cs water.gro -o waterbox.gro -maxsol 768
-radius 0.21 -p dppc.top
768 waters are added, resulting in the "waterbox.gro".
However, the "dppc.top" is not updated for its "[ molecules ]" section. I can
of course manually add that. But why it
I can dual boot windows and Ubuntu on my computer but since I'm doing
docking with AutoDock I'm using windows.
What is your opinion should I use Ubuntu or Windows 10 for Gromacs MD
simulations?
Will I face trouble if I use Windows 10 for Gromacs MD simulation.
On Sun, Jan 20, 2019 at 2:38 PM Mark
Dr. Mark Abraham, thank you so much for your help.
That meaning that in the NPT equilibration without position restrains
the refcoord_scaling should not be present at all in the mdp file*?*
Thank you in advance.
Olga
בתאריך יום א׳, 20 בינו׳ 2019 ב-11:06 מאת Mark Abraham <
Hi,
No, at run time.
Mark
On Fri., 18 Jan. 2019, 20:06 paul buscemi, wrote:
> Szilard,
>
> Is the environmental variable set at build ?
>
> thanks
> Paul
>
> > On Jan 18, 2019, at 12:36 PM, Szilárd Páll
> wrote:
> >
> > Hi,
> >
> > The CUDA runtime tries (and AFAIK has always tried) to be
Hi,
There's some support for Windows and it works pretty well. Installation is
covered in the installation guide, but it can be a bit trickier than on
Linux.
Mark
On Sun., 20 Jan. 2019, 06:19 Quin K, wrote:
> I hope to use windows 10 to run gromacs md simulation. Will i face any
> trouble
Hi,
If you're not using position restraints then options that affect how they
work are inactive.
Mark
On Sun., 20 Jan. 2019, 09:46 Olga Press, wrote:
> Dear gromacs users,
>
> I perform membrane-protein simulation and used the same mdp files as
> suggested by the tutorial of Dr. Justin
Dear gromacs users,
I perform membrane-protein simulation and used the same mdp files as
suggested by the tutorial of Dr. Justin Lemkul with one exception of
changing the correct parameters for charmm36ff as suggested
by gromacs manual.
I performed 10ns of *NVT equilibration with position
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