Hi all,
Sorry about the last incomplete mail.I have a trajectory of 300 ns for a
membrane protein. I want to sample native/non-native conformations and
compare across various systems. My question is can parameters like
number/occupancy of hbonds or the time evolution of helical residues
(output fr
Hi all,
I have a trajectory of 300 ns for a membrane protein. I want to sample
native/non-native conformations and compare across various systems. My
question is can parameters like number/occupancy of hbonds or the time
evolution of helical residues (output from gmx do_dssp) be clusterized
using
Hello Justin, Thanks for your answer. So can ethanol molecule be
supported by 2013-Drude force field in GMX, if any, how to get its itp file?
Thanks a lot.
==Date: Thu, 26 Oct 2017
07:08:33 -0400From: Justin Lemkul To:
gmx-users@groma
I want to determine permeability of drug molecules through various lipid
membranes.
Building the membrane i am able to do with the kalp-dppc tutorial, but for
placing the drug molecule above the membrane i am not getting proper
solution.
So can someone suggest how to place the drug molecule above
On 10/26/17 1:58 PM, Hoa Trinh wrote:
Dear Mark & Justin,
Thank you very much. Hum, the name of variable nbonds is a bit misleading.
Well, you'll find many of those in every software package, and
n_elements_of_type_and_atom_index is harder to type than nbonds :)
An explanation of how thing
Dear Mark & Justin,
Thank you very much. Hum, the name of variable nbonds is a bit misleading.
*Lan Hoa*
2017-10-26 6:10 GMT-05:00 Justin Lemkul :
>
>
> On 10/26/17 1:56 AM, Hoa Trinh wrote:
>
>> Hi all,
>> I am trying to look into the source code of Gromacs 5.0.7 to see how
>> Gromacs calculate
Hi,
My simulation results for viscosity calculation strongly depends on the
chosen amplitudes of the acceleration profiles in the .mdp file (!?). How
to estimate acceleration amplitude values?
appreciate if someone can answer,
Best regards
--
Gromacs Users mailing list
* Please search the archi
Thanks - good to know that there is no clear winner between GCC and Intel
with GROMACS performance.
As I'm building the software on behalf of a number of other people, and so
don't have a typical simulation to do speed tests with, I can happily pick
the lower-risk option and switch to GCC.
R
Dear all,
I have found density of states (Dos) of a protein ligand system from gmx dos
command of gromacs. I would like to know if it employs the same principle
component analysis as used in g_covar. If not what are the differences.
Also the Dos obtained from gmx dos has solid and diffusive co
Hi,
It might, but Intel also works on the gcc and llvm compilers and their core
business is hardware, not selling the compiler. Our experience on non-Phi
is that performance is often quite close, but your actual hardware and
simulation are probably also going to affect which compiler implementatio
On 10/26/17 10:13 AM, Hermann, Johannes wrote:
Hi Justin,
yes everything is clear in the manual.
What I now get are lincs warnings for the OW-HW1 and OW-HW2 bond:
(exemplary for the OW-HW1 bond):
LINCS WARNING in simulation 1
relative constraint deviation after LINCS:
rms 0.317574, max 0.54
On 10/26/17 10:09 AM, Simon Kit Sang Chu wrote:
Hi everyone,
Last time, I mentioned missing parameter for neutral terminal dihedral and
U-B type. After some debugging, I am still not sure what the cause was. I
hope providing more information could help to resolve the issue. I am using
CHARMM36
Hi Mark,
Many thanks for the reply.
Am I going against the flow by using the Intel compiler with GROMACS? I've
been using it so far because of - the potentially foolhardy idea - that it
might generate a faster executable than GCC on modern Intel processors.
Best,
Mark
On Thu, 26 Oct 2017,
Hi,
I would look back to the literature to find what terminal PRO has CMAP
defined.
Mark
On Thu, 26 Oct 2017 16:10 Simon Kit Sang Chu wrote:
> Hi everyone,
>
> Last time, I mentioned missing parameter for neutral terminal dihedral and
> U-B type. After some debugging, I am still not sure what
Hi,
Thanks for the report - we should look into that combination. It's highly
likely that there's some minor issue that different optimization capability
is creating or exposing. The functionality covered by that test is only
used for a few analysis tools, and the fact that gcc passes fine suggest
Hi Justin,
yes everything is clear in the manual.
What I now get are lincs warnings for the OW-HW1 and OW-HW2 bond:
(exemplary for the OW-HW1 bond):
LINCS WARNING in simulation 1
relative constraint deviation after LINCS:
rms 0.317574, max 0.547778 (between atoms 1 and 2)
bonds that rotated mo
Hi everyone,
Last time, I mentioned missing parameter for neutral terminal dihedral and
U-B type. After some debugging, I am still not sure what the cause was. I
hope providing more information could help to resolve the issue. I am using
CHARMM36 forcefield.
Brief summary of the problem -
No dihe
On 10/26/17 9:19 AM, Hermann, Johannes wrote:
Hi Justin,
thanks for the quick response! Ahhh! I looked into the manual for [
settles ] and "i j funct length" is kind of misleading.
So this should work, right?
[ constraints ]
; i j funct length
1 2 1 0.09572
1 3 1 0.09572
2
Hi Justin,
thanks for the quick response! Ahhh! I looked into the manual for [
settles ] and "i j funct length" is kind of misleading.
So this should work, right?
[ constraints ]
; i j funct length
1 2 1 0.09572
1 3 1 0.09572
2 3 1 0.15139
Thanks, Justin!
All the best
On 10/26/17 8:58 AM, Hermann, Johannes wrote:
Dear Gromacs Users, dear Justin,
I am using the tip3p water model and I want to restrain one single
water molecule. I found Justins reply in the mailing list a few years
ago:
/If you want to restrain a single water molecule, it needs to be
def
Dear Gromacs Users, dear Justin,
I am using the tip3p water model and I want to restrain one single water
molecule. I found Justins reply in the mailing list a few years ago:
/If you want to restrain a single water molecule, it needs to be defined as />>/its own [moleculetype] or as a part of
Hi there,
Is there a recommended compiler for GROMACS, please?
I'm trying to validate my install on a CentOS 7.4 Intel Broadwell system
by running the tests shipped in the GROMACS source tar ball (and the
separate regression tests).
If I use GCC (4.8.5 or 7.2.0), everything passes but, if I
Hello, I have a gro file that contains a cubic system
(water+membrane+protein). Is there a way to align the box with the three
principal axes x y z? I see that with editconf -princ I can align it to x,
but y and z are pointing towards the corner of the box instead of being
aligned with the respecti
Damn, you're absolutely right..Thank you very very much! Now it is working.
We were using something done by others many years ago, we believed it was
fine (big mistake).
Thank you again!
On Thu, Oct 26, 2017 at 1:07 PM, Justin Lemkul wrote:
>
>
> On 10/26/17 7:05 AM, Elisa Pieri wrote:
>
>> Tha
On 10/26/17 1:56 AM, Hoa Trinh wrote:
Hi all,
I am trying to look into the source code of Gromacs 5.0.7 to see how
Gromacs calculate bonded interactions. For example, to calculate bond
interaction between 2 atoms, there is the function (gmxlib/bondfree.c):
real bonds(int nbonds, ...)
{
On 10/26/17 2:08 AM, Chamikara Herath wrote:
I need to run a MD simulation with two ligands
01. Natural Substrate (GTP)
02. Allosteric drug candidate bounds closer to the substrate binding pocket.
single itp file was created , combining both ligands using Swiss pharm for
CHARMM force field.
On 10/26/17 3:20 AM, limingru wrote:
Hi gmx users or developers, I am trying to do some Drude
polarizable simulations using GMX. How to convert coordinate file (e.g pdb)
into Drude format file? Thanks in advance.
There is no special "Drude format" for coordinate files. I
On 10/26/17 7:05 AM, Elisa Pieri wrote:
Thank you very much for the answers! We made the modifications you
suggested and now the error changed.
Now we have this problem: we have an ALA residue, linked to a LYS. The LYS
is linked to a retinal moiety; for this, we created a "new" residue called
Thank you very much for the answers! We made the modifications you
suggested and now the error changed.
Now we have this problem: we have an ALA residue, linked to a LYS. The LYS
is linked to a retinal moiety; for this, we created a "new" residue called
"RET" which includes LYS+retinal. But now, G
In the line you have added into the ffnonbonded.itp it looks like the numbers
for the LJ parameters have a comma rather than a point. So 2,47135e-01 rather
than 2.47135e-01. I imagine this is causing the too few parameters on line
warning
Cheers
Tom
Fro
Hi,
I don't recall whether lower case is supported here, I imagine it might not
be because historically FORTRAN-era force fields used all caps. You could
try using only upper case.
Mark
On Thu, Oct 26, 2017 at 11:53 AM Elisa Pieri
wrote:
> Hello again,
>
> we are trying to add Amber lipids to
Hello again,
we are trying to add Amber lipids to the Amber94 force field (actually, it
is a version where a few years ago we added a ligand). We used pdb2gmx as
"pdb2gmx -f file.pdb" and we successfully created a conf.gro and topol.top
file (and posre.itp and top.itp per lipid molecule). Then, wh
Hi gmx users or developers, I am trying to do some Drude
polarizable simulations using GMX. How to convert coordinate file (e.g pdb)
into Drude format file? Thanks in advance.
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