Sorry for the duplicate post.
Hi Users
I am performing a simulation for a bonded metal-protein complex system.
Here I am aware of adding the essential parameters in ffbonded .itp. The
force constant value (kb) in the ffbonded.itp file is calculated using
Gaussian. I would like to clarify the meth
Please see gmx sorient command from the manual.
Regards
Nabin
El mié., 12 sept. 2018 a las 9:23, rose rahmani ()
escribió:
> Hi,
>
> Hiw can i calculate angle between two plane?(HOH plane of water and surface
> plane or perpendicular axis to it? How should i make an index for defining
> HOH plane
Test timeouts are strange, Is the machine you're running on busy with other
jobs?
Regarding the regressiontest failure, can you share
tests/regressiontests*/complex/octahedron/mdrun.out
please?
--
Szilárd
On Thu, Sep 13, 2018 at 8:49 PM Phuong Tran wrote:
> Hi all,
>
> I have been trying to i
Hi Justin,
Any comment please one the initial question of the current ticket?
Thanks.
Alex
On Thu, Sep 13, 2018 at 5:04 PM Justin Lemkul wrote:
>
>
> On 9/13/18 4:34 PM, Huang, Tina wrote:
> > How do I unsubscribe? :)
>
> In the footer of every email across the list:
>
> * For (un)subscribe req
On 9/13/18 4:34 PM, Huang, Tina wrote:
How do I unsubscribe? :)
In the footer of every email across the list:
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail togmx-users-requ...@gromacs.org.
-Justin
Thanks!
Tina
On
How do I unsubscribe? :)
Thanks!
Tina
On Thu, Sep 13, 2018 at 10:45 AM, Alex wrote:
> Dear all,
> I wonder how tau-p/tau-t can affect on simulation and how it should be
> chosen wisely according to the system of study?
>
> Also, the performance of GMX-2018.2 is around 10 ns/day for NVT/NpT
> eq
Hi all,
I have been trying to install Gromacs on our GPU workstation that has CUDA
9.0
It went well but 'make check' have failed so far on either 2018.3 or 2018.2
versions.
anybody know how to resolve it?
Please see the error below.
Thank you,
-T
Test project /home/user/Softwares/gromacs-2018.3/b
Dear all,
I wonder how tau-p/tau-t can affect on simulation and how it should be
chosen wisely according to the system of study?
Also, the performance of GMX-2018.2 is around 10 ns/day for NVT/NpT
equilibration of a system while the performance increases to around 18
ns/day for the NVT production
Dear all,
Can anyone tell me the command used for calculating the population density
plot between Ree and Rg? As I have calculated the Ree and Rg value from gmx
polystat command now, i want to plot population density between Ree and Rg.
Your help will be appreciated.
Thank u
-
Ishrat Jahan
Research
Thank you dear justin, finally you answer me;)
On Thu, 13 Sep 2018, 16:59 Justin Lemkul, wrote:
>
>
> On 9/13/18 7:55 AM, rose rahmani wrote:
> > Hi,
> >
> > I recieved an email from GROMACS, says the message is too big(because of
> > many replies). So what should i do to continue my discussion?
On 9/13/18 7:55 AM, rose rahmani wrote:
Hi,
I recieved an email from GROMACS, says the message is too big(because of
many replies). So what should i do to continue my discussion?
Cut out old, unimportant text.
-Justin
--
==
Justin A. Lemkul
Hi,
I recieved an email from GROMACS, says the message is too big(because of
many replies). So what should i do to continue my discussion?
Best
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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On 9/13/18 7:56 AM, Matteo Busato wrote:
Hi to everyone,
I am trying to perform a calculation on a cluster, where Gromacs 5.1.4 was
compiled, using a polarizable force field carrying shells. Since domain
decomposition can not be used, I was trying to launch mdrun with the -ntmpi 1
-ntomp
Hi to everyone,
I am trying to perform a calculation on a cluster, where Gromacs 5.1.4 was
compiled, using a polarizable force field carrying shells. Since domain
decomposition can not be used, I was trying to launch mdrun with the -ntmpi 1
-ntomp=number-of-cores options as Justin stated in a
On 9/13/18 1:20 AM, Rakesh Mishra wrote:
I do not believe .
Because if I run multiple simulation of pulling with the same system and
with the
same inputs then almost we are getting similar force/time curve.
While we are getting different curve if we are saving position coordinates
or energy
c
On 9/13/18 6:17 AM, marzieh dehghan wrote:
Hi
Dear all
I used charm36 and cgenff (http://mackerell.umaryland.edu/charmm_ff.shtml)
to convert str format of ligand to itp format. when I used the following
command:
python cgenff_charmm2gmx.py LIG lig.mol2 lig.str charmm36-jul2017.ff/
I confront
Hi Marzieh,
I don't think the error is related to python version, but the naming of the
files. Maybe the script needs that your input files are also named as LIG.str
and LIG.mol2, something like that.
What I do know about the script when using it before, is that it requires an
older version of
Hi
Dear all
I used charm36 and cgenff (http://mackerell.umaryland.edu/charmm_ff.shtml)
to convert str format of ligand to itp format. when I used the following
command:
python cgenff_charmm2gmx.py LIG lig.mol2 lig.str charmm36-jul2017.ff/
I confront this error:
NOTE1: Code tested with python 2.
Hi I think you should check this paper:Åqvist J, Medina C, Samuelsson JE. A
new method for predicting binding affinity in computer-aided drug design.
Protein Engineering, Design and Selection. 1994 Mar 1;7(3):385-91.It explains
everything and gives example of use.And yes with different water mo
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