Dear gromacs users list,
I noticed that gromacs can perform simulations with an implicit solvent
model using a GBSA method. Is it compatible with the CHARMM22 force field?
Thanks,
Gianluca
-
Gianluca Interlandi, PhD gianl
I would like to ask whether it is possible to use in Gromacs the CHARMM
parameters for silicates. More generally, is it easy to convert CHARMM
parameter and topology files to the gromacs format?
Thanks,
Gianluca
-
Gianluca Interlandi
a 0-steps MD and read out the
energy? I know that this would have a big overhead in a MC simulation, but
it might be worth trying.
Thanks,
Gianluca
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685
://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
On Mon, Jan 23, 2012 at 11:39 PM, Gianluca Interlandi
gianl...@u.washington.edu wrote:
Hi!
I would like
://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
On Tue, Jan 24, 2012 at 12:36 AM, Gianluca Interlandi
gianl...@u.washington.edu wrote:
Thanks Enrico!
Just wondering. How fast is it? Calling gromacs must have a
lot of overhead. Also, do you call mdrun or does g_energy
Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile -
http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
On Tue, Jan 24, 2012 at 12:36 AM, Gianluca Interlandi
gianl...@u.washington.edu wrote:
Thanks Enrico!
Just wondering. How fast
long interval simply a waste of time or
can it actually introduce artefacts?
Thanks,
Gianluca
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http
, Gianluca Interlandi wrote:
Hi,
I have been going through the How-to for REMD in gromacs:
http://www.gromacs.org/Documentation/How-tos/REMD
Is there a recommended value for the exchange interval and does it depend
on system size? For example, is an interval of 100 ps appropriate for a
sytem
Hi David,
I am actually performing Simulated Tempering which is the same as RE
except that it is in series. But I guess that the same thinking concerning
exchange interval still applies.
Gianluca
On Thu, 26 Jan 2012, David van der Spoel wrote:
On 2012-01-26 06:37, Gianluca Interlandi
Boelelaan 1081a
1081HV AMSTERDAM, the Netherlands
Room P 2.75
E: r.p...@vu.nl
T: +31 20 598 76 12
F: +31 20 598 76 10
=
From: Gianluca Interlandi [gianl...@u.washington.edu]
Sent: 24 January 2012 21:20
=
From: Gianluca Interlandi [gianl...@u.washington.edu]
Sent: 30 January 2012 17:36
To: Pool, R.
Cc: Discussion list for GROMACS users
Subject: RE: [gmx-users] Monte Carlo with Gromacs and implicit solvent
Hi René,
I want to perform simulations of a protein near a surface, for example
silicates
it
should do. Does anyone have experience in calculating hydrogen bonds with
version 3.3.1?
Thanks a lot,
Gianluca
-
Dr. Gianluca Interlandi [EMAIL PROTECTED]
+1 (206) 685 4432
+1 (206) 714 4303
not correspond to the number of
hbonds in hbmap.xpm. But maybe there is an easier way to do this.
Thanks,
Gianluca
-
Dr. Gianluca Interlandi [EMAIL PROTECTED]
+1 (206) 685 4432
+1 (206) 714 4303
-
Dr. Gianluca Interlandi [EMAIL PROTECTED]
+1 (206) 685 4432
+1 (206) 714 4303
http://biocroma.unizh.ch/gianluca/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA
-
Dr. Gianluca Interlandi [EMAIL PROTECTED]
+1 (206) 685 4432
+1 (206) 714 4303
http://biocroma.unizh.ch/gianluca/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A
. That is what was done in the Bjelkmar et al paper
where CHARMM27 was implemented in GROMACS
(http://pubs.acs.org/doi/full/10.1021/ct900549r).
Best wishes
James
On 24 Aug 2013, at 23:08, Gianluca Interlandi gianl...@u.washington.edu wrote:
Hi!
I am running explicit solvent simulations
...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist
have been asked many times already, but I
could not find an answer.
Thanks,
Gianluca
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
http://artemide.bioeng.washington.edu/
Research Scientist at the Department
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http
Hi!
Just wondering whether gromacs has (or plans to implement) a correction
for the loss of long range LJ interactons? Something similar to
LJcorrection in NAMD or IPS in CHARMM.
Thanks!
Gianluca
-
Gianluca Interlandi, PhD gianl
for 5.0
Mark
On Aug 28, 2013 8:36 AM, Gianluca Interlandi
gianl...@u.washington.edu
wrote:
Hi!
Just wondering whether gromacs has (or plans to implement) a correction
for the loss of long range LJ interactons? Something similar to
LJcorrection in NAMD or IPS in CHARMM.
Thanks!
Gianluca
it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu
use a shorter cutoff.
Gianluca
On Wed, 28 Aug 2013, Justin Lemkul wrote:
On 8/28/13 7:28 PM, Gianluca Interlandi wrote:
Thanks for your replies, Mark. What do you think about the current DispCorr
option in gromacs? Is it worth it trying it? Also, I wonder whether using
DispCorr for LJ + PME
the system is affected.
Gianluca
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
to the list. Use the www interface
or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
And also, gromacs does not seem to use the same switching function as
CHARMM. Has it been tested how much this affects replication of the
original CHARMM MM energies?
Gianluca
On Thu, 29 Aug 2013, Gianluca Interlandi wrote:
Of course, if accuracy is not in question then performance dominates
Yes, I've seen that thread before. My feeling is that simulating membranes
with the CHARMM36 FF is a different story. It's good to be aware of that.
Gianluca
On Thu, 29 Aug 2013, Justin Lemkul wrote:
On 8/29/13 5:15 PM, Gianluca Interlandi wrote:
Of course, if accuracy is not in question
been interesting if they had done the comparions using the
recommended 10/12/14 cutoff (although PME would have been compulsory
since gromacs Shift function completely differs from CHARMM SHIFT).
Gianluca
On Thu, 29 Aug 2013, Justin Lemkul wrote:
On 8/29/13 5:33 PM, Gianluca Interlandi
to find an alternative :)
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
. Is there an equivalent flag for cmake that corresponds to
--enable-shared?
Thanks,
Gianluca
On Sat, 31 Aug 2013, Gianluca Interlandi wrote:
Hi!
I am currently using mdrun -rerun in order to get the energy of a system to
be used in a Monte Carlo algortihm. A while ago, I was pointed to Grompy
Thanks Justin.
I have been wondering where I can find all options of cmake (./configure
--help used to print all possible options, whereas cmake --help prints out
just the usage of cmake itself).
Gianluca
On Sat, 31 Aug 2013, Justin Lemkul wrote:
On 8/31/13 2:16 PM, Gianluca Interlandi
it be
that libmdrun.so is replaced by libmd.so in version 4.6.3? Does the
command mdrun call libmd.so?
Thanks,
Gianluca
On Sat, 31 Aug 2013, Justin Lemkul wrote:
On 8/31/13 2:16 PM, Gianluca Interlandi wrote:
After reading a bit more in the grompy directory, I found that the file
__init__.py
, Gianluca Interlandi wrote:
I complied gromacs 4.6.3 with -DBUILD_SHARED_LIBS=ON. The only libraries
that I
find are:
libmd.so libgmxana.so libgmxpreprocess.so libgmx.so
which are also produced without specifying -DBUILD_SHARED_LIBS=ON There is
no
library called libmdrun.so like the one used in grompy
Dear Mark,
Thank you very much for the enlightment. I will look into named pipes.
This might be appropriate since I'm calling mdrun from a TCL script in
VMD.
Gianluca
On Sun, 1 Sep 2013, Mark Abraham wrote:
On Sat, Aug 31, 2013 at 9:33 PM, Gianluca Interlandi
gianl...@u.washington.edu
...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist
On 9/3/13 3:10 PM, Gianluca Interlandi wrote:
Also, why in vacuo? At least turn on an implicit solvent model.
I can think of reasons to study molecular interactions in vacuo via pulling.
I'm sure there are.
G
Why is solvent (explicit or implicit) an absolute requirement?
-Justin
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A
= 1000
; ENERGY MINIMIZATION OPTIONS =
emtol= 0.1
emstep = 0.01
nstcgsteep = 1000
Thanks!
Gianluca
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
Is there a way to tell from the log file whether positional restraints are
really activated or not?
Thanks,
Gianluca
On Sun, 3 Nov 2013, Justin Lemkul wrote:
On 11/3/13 12:38 AM, Gianluca Interlandi wrote:
Is it possible to use position restraints:
define = -DPOSRES
during
step at the start of equilibration, even where there were no atomic
clashes. Maybe the system was just unlucky with generating velocities,
though :-)
Mark
On Aug 28, 2013 7:16 AM, Gianluca Interlandi gianl...@u.washington.edu
wrote:
How important is it to do gentle heating (using simulated
=
; rotates over more degrees than =
lincs_warnangle = 30
; Convert harmonic bonds to morse potentials =
morse= no
On Mon, 4 Nov 2013, Justin Lemkul wrote:
On 11/4/13 2:25 PM, Gianluca Interlandi wrote:
Dear Mark,
Sorry for replying to an older thread. We are trying
I wonder whether increasing the surface tension parameter
sa-surface-tension might solve the problem with the protein unfolding.
Thanks,
Gianluca
On Mon, 4 Nov 2013, Gianluca Interlandi wrote:
Hi Justin,
We are using infinite cutoffs (all vs all). Here is the mdp file for the
heating
Does it make more sense to use nose-hoover or v-rescale when running in
implicit solvent GBSA? I understand that this might be a matter of
opinion.
Thanks,
Gianluca
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A
On Sat, 9 Nov 2013, Gianluca Interlandi wrote:
Just to chime in. Here is a that paper might be helpful in understanding
the role of cuoffs in the CHARMM force field:
AU STEINBACH, PJ
BROOKS, BR
AF STEINBACH, PJ
BROOKS, BR
TI NEW SPHERICAL-CUTOFF METHODS FOR LONG-RANGE FORCES
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