Hi,
Your working directory is the one in which you are doing your work. You are
making a copy of the normal force field folder, so that next time you use
it, you know it is unchanged from what GROMACS provides. Having made the
copy, edit the files in the copy.
Mark
On Sun, Jul 22, 2018, 09:49
dear all
I am a new user,I was doing this
tutorial(http://www.mdtutorials.com/gmx/membrane_protein/index.html) it said
{To use the parameters in lipid.itp, we will have to make some changes to our
pre-packaged GROMOS96 53A6 force field files (in $GMXLIB/gromos53a6.ff). Make a
copy of
Dear Experts,Is there any tutorial available online for
understanding procedure to calculate diffusion coefficient from umbrella
sampled force and position trajectory data. The formula for diffusion is given
as D()=variance(z)/tau. Numerator is variance of z (or
Hi, is there a tutorial for importing fully charged non-peptid topologies for
the AMBER FF ISBN type to GMX somewhere ?
Thanks
Sergio Manzetti
Fjordforsk AS
Midtun
6894 VangsnesNorge
Org.nr. 911 659 654
Tlf: +47 57695621Økolab | Nanofactory |
On 6/21/16 1:49 AM, amitbe...@chemeng.iisc.ernet.in wrote:
Hello,
The summary_distances.dat file contains only one column ( the column for
COM is missing).
I am using GROMACS 5.1.2. How to solve this issue.
I feel like I've answered this same exact question several times in the last
week.
Hello,
The summary_distances.dat file contains only one column ( the column for
COM is missing).
I am using GROMACS 5.1.2. How to solve this issue.
Regards,
Amit Behera
Research Scholar,
Dept. of Chemical Engineering,
IISc
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On 6/20/16 4:08 PM, Kyle Titus-Glover wrote:
Sure, I can gather up the files and send them in a compressed folder to you
school email if that's ok.
Yes. The sequence of commands (in an executable script) is also essential. A
dump of files is only a small part of the equation.
-Justin
Sure, I can gather up the files and send them in a compressed folder to you
school email if that's ok.
Kyle Titus-Glover
On Mon, Jun 20, 2016 at 3:45 PM, Justin Lemkul wrote:
>
>
> On 6/20/16 3:11 PM, Kyle Titus-Glover wrote:
>
>> However, I did look into system_shrink1.gro
On 6/20/16 3:11 PM, Kyle Titus-Glover wrote:
However, I did look into system_shrink1.gro and saw that the file was
missing the peptides and that 2 DPPC molecules still remained undeleted.
Should I manually correct the coordinate file?
No, you should correct whatever it is that you're doing
However, I did look into system_shrink1.gro and saw that the file was
missing the peptides and that 2 DPPC molecules still remained undeleted.
Should I manually correct the coordinate file?
On Mon, Jun 20, 2016 at 3:09 PM, Kyle Titus-Glover wrote:
> I tried restarting the whole
I tried restarting the whole process to go back and carefully look and make
sure that nothing was spelled right. Bu I still get the same error.
On Mon, Jun 20, 2016 at 2:36 PM, Justin Lemkul wrote:
>
>
> On 6/20/16 2:32 PM, Kyle Titus-Glover wrote:
>
>> Hey everyone,
>>
>>
On 6/20/16 2:32 PM, Kyle Titus-Glover wrote:
Hey everyone,
I've been working on the Justin Lemkul's 2nd tutorial and just can't seem
to get past 2. packing the lipids around the protein and 3. solvating with
water. The follow the instructions step by step but for some reason as I
try to run
Hey everyone,
I've been working on the Justin Lemkul's 2nd tutorial and just can't seem
to get past 2. packing the lipids around the protein and 3. solvating with
water. The follow the instructions step by step but for some reason as I
try to run EM with
gmx grompp -f minim.mdp -c
Hey everyone,
I've been working on the Justin Lemkul's 2nd tutorial and just can't seem
to get past 2. packing the lipids around the protein and 3. solvating with
water. The follow the instructions step by step but for some reason as I
try to run EM with
gmx grompp -f minim.mdp -c
your two dummy types appear to be identical
> you can define just one.
>
> Cheers,
> Hannes.
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Sebast
s lambda=1 corresponds to "typeB", so my
> >>> transformation is "XX" -> "Na+", "Cl-" -> "XX"
> >>>
> >>> Thanks a bunch,
> >>> Sebastian
> >>>
> >>>
> >>>
&
>>>
>>> On 30.11.2015 17:30, hannes.loeff...@stfc.ac.uk wrote:
>>>> Dear Sebastian,
>>>>
>>>> I have some trouble reading your top file in my web browser but I
>>>> think your transformations are IPX->Na+, IMX->Cl-. So you would
>>>
eading your top file in my web browser but I
> > > think your transformations are IPX->Na+, IMX->Cl-. So you would
> > > have to reverse the columns for the first atom. As your two dummy
> > > types appear to be identical you can define just one.
> > >
&g
efine just one.
> >
> > Cheers,
> > Hannes.
> >
> > ________
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of
> > Sebastian Stolzenberg [s.sto
anual
> describes how to set up the A and the B state of a molecule.
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Sebastian
> Stolzenberg [s.stolzenb.
le.
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Sebastian
> Stolzenberg [s.stolzenb...@fu-berlin.de]
> Sent: 29 November 2015 13:11
> To: gromacs.org_gmx-user
Thanks, that did the trick! Now everything works fine.
Am 29.11.2015 um 12:00 schrieb
gromacs.org_gmx-users-requ...@maillist.sys.kth.se:
On 11/27/15 5:36 PM, Matthias Kiesel wrote:
Hi All,
I am currently doing the umbrella sampling tutorial by Justin Lemkul, but i have
a problem with
Dear Gromacs experts,
I am looking for a Gromacs tutorial to perform a "dual" alchemical
transformation in a water box, i.e. a mutation or any other alchemical
transformation, in which:
the nonbonded interactions between the environment and a molecule A
disappear as lambda goes from 0 to 1,
er 2015 13:11
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] tutorial for "dual" alchemical transformation in gromacs?
Dear Gromacs experts,
I am looking for a Gromacs tutorial to perform a "dual" alchemical
transformation in a water box, i.e. a mu
On 11/27/15 5:36 PM, Matthias Kiesel wrote:
Hi All,
I am currently doing the umbrella sampling tutorial by Justin Lemkul, but i have
a problem with creating the right configurations for the umbrella sampling run.
After running the first pull simulation and the given perl script the com
Hi All,
I am currently doing the umbrella sampling tutorial by Justin Lemkul,
but i have a problem with creating the right configurations for the
umbrella sampling run. After running the first pull simulation and the
given perl script the com distances don´t go from 0.5nm to 5nm, instead
Dear all,
I am trying to follow the tutorial:
http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html
Part:
ANALYSIS OF DYNAMICS AND TIME-AVERAGED PROPERTIES
In the command:
trjconv -f traj_helix.xtc -o traj_helix_10-50ns.xtc -n
_peptide_index.ndx -pbc nojump -dt 100 -b 1
what is
Dear all,
I am trying to follow the tutorial:
http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html
Part:
ANALYSIS OF DYNAMICS AND TIME-AVERAGED PROPERTIES
In the command:
trjconv -f traj_helix.xtc -o traj_helix_10-50ns.xtc -n
_peptide_index.ndx -pbc nojump -dt 100 -b 1
what is
Hi Urszula,
I suspect it's a naming inconsistency or the tutorial got garbled. Maybe
you can contact Adrien Melquiond about this.
Cheers,
Tsjerk
On Thu, Oct 15, 2015 at 1:02 PM, Urszula Uciechowska <
urszula.uciechow...@biotech.ug.edu.pl> wrote:
> Dear all,
>
> I am trying to follow the
Dear Justin,
I hope all thing will be on its road soon :)
Tuong Vy
2015-06-02 23:12 GMT+09:00 Justin Lemkul jalem...@vt.edu:
All,
Yesterday we experienced a hardware failure on the server that hosts my
GROMACS tutorials. We are aware of the issue and are going to be setting
up a new
All,
Yesterday we experienced a hardware failure on the server that hosts my GROMACS
tutorials. We are aware of the issue and are going to be setting up a new
server. The tutorials may end up on this new server or another; I haven't
decided yet. For the next few days, the tutorials will
On 3/19/15 12:30 AM, Rajneet kaur Saini wrote:
Greetings,
I want to install gromacs on window 7. but i don't know the exact
procedure.could you please explain me the procedure to install gromacs on
window.
Thanking you in anticipation
Greetings,
I want to install gromacs on window 7. but i don't know the exact
procedure.could you please explain me the procedure to install gromacs on
window.
Thanking you in anticipation
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Gromacs Users mailing list
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Hi Justin,
Do you plan to keep the Gromacs 4.x versions of your tutorials (which by
the way are excellent) around for a little longer as well?
From my experience It will still take quite some time until Gromacs 5 is
available on most Clusters and Linux-package repositories, whereas the
Gromacs 4
On 7/9/14, 2:40 PM, Oliver Stueker wrote:
Hi Justin,
Do you plan to keep the Gromacs 4.x versions of your tutorials (which by
the way are excellent) around for a little longer as well?
From my experience It will still take quite some time until Gromacs 5 is
available on most Clusters and
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