Hi,
On Fri, Sep 18, 2015 at 6:27 AM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> Dear Users:
>
> I have a system with many distance restraints, designed to maintain
> helical character, e.g.:
> [ distance_restraints ]
> 90 33 1 1 2 2.745541e-01 3.122595e-01 999 1.0
> 97 57 1 2 2 2.8
Hi all,
I am simulating a membrane protein in DPPC in order to insert it in the
bilayer. I did a previous run during 2 us and I saw major changes in the
secondary structure. Now I want to use an elastic network in order to
preserve the overall secondary structure.
It is possible to build an
Hello gmx users,
I have a two-socket (8 physical cores each, and with hyperthreading 32
cores system) with 2 gpus. I want to run two independent simulations using
16 threads and a single GPU.
I tried the -pin on and -pinoffset 0 for the first instance of mdrun and
-pin on and -pinoffset 8 for th
Hi,
pinoffset 0 and 16 should be correct, these should place threads on what's
shown as "CPU" idx 1-8,17-24 and 9-16,25-32, resp.
Cheers,
--
Szilárd
On Fri, Sep 18, 2015 at 11:59 AM, Deva Priya
wrote:
> Hello gmx users,
>
> I have a two-socket (8 physical cores each, and with hyperthreading 3
On 9/18/15 12:20 AM, Maryam Kowsar wrote:
Thaks justin!
I did it several times and it worked. But now when i want to add some
neutral gas or heavy atoms it stops me with the error that the atom is not
defined. I dont know where i make a mistake.
Neither does anyone here, because you haven't
Hi Andreas,
I use OPLSAA myself, and although it gets the wrong figures for the surface
potential and other interfacial properties, it is a known bias and you know
in which direction your results are going wrong.
IMHO, switching to other non-polarizable forcefield wouldn't work either,
since most
Hello,
How can I restrain the position of one group of molecules, but let them
interact with other molecules free to move within the system?
Thanks,
Anand Dharia
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Hello,
I am wondering if there is any built-in method that Gromacs may have to
quantify the extent of clustering between protein molecules.
Thanks,
Anand Dharia
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On 9/18/15 7:30 PM, ANAND AMITKUMAR Dharia wrote:
Hello,
How can I restrain the position of one group of molecules, but let them
interact with other molecules free to move within the system?
Position restraints do not affect nonbonded interactions.
-Justin
--
=
On 9/18/15 7:46 PM, ANAND AMITKUMAR Dharia wrote:
Hello,
I am wondering if there is any built-in method that Gromacs may have to
quantify the extent of clustering between protein molecules.
There are plenty of things you can calculate. Consult Chapter 8 of the manual.
gmx cluster, gmx cl
Dear Mark:
you are correct. If I get rid of the gmx_fatal call then everything seems to
work just fine.
In the file src/gmxlib/disre.c , I got rid of the following code, which starts
on line 147 of gmx 4.6.7:
if (dd->dr_tau != 0 || ir->eDisre == edrEnsemble || cr->ms != NULL ||
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