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 IN
x-users
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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
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
=
; 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
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"
wrote:
How important is it to do gentle heating (using simulated annealing) with
G
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 an
= 1000
; ENERGY MINIMIZATION OPTIONS =
emtol= 0.1
emstep = 0.01
nstcgsteep = 1000
Thanks!
Gianluca
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Gianluca Interlandi, PhD gianl...@u.washington.edu
ling_Lists
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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, Seattl
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
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Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://a
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
wrote:
Thanks for lo
, 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
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
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
;configure". 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 Car
ut
until it's released I need to find an alternative :)
-----
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist at the Depar
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
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 i
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
uests to the list. Use the www interface
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-
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206
that one should test how much 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 Depar
ust 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 +
e www interface
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---------
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
ht
nluca Interlandi"
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
--**--
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
-
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
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 of
users-requ...@gromacs.org.
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-----
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Resear
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 wrote:
Hi!
I am running explicit solvent simulations with the CHARMM force field
implemented in gromacs 4.6.3. For
-
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
F: +31 20 598 76 10
=
____
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, f
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
To
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
, 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 with
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
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
wrote:
Thanks Enrico!
Just wondering. How fast is it? Calling gromacs must have a
/rodrigo-faccioli/7/589/a5
On Tue, Jan 24, 2012 at 12:36 AM, Gianluca Interlandi
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
evaluate the energy?
Gianluca
On Tue, 24 Jan
atics
http://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
wrote:
Hi!
I would like to use gromacs
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
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
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
;.
Thanks a lot for your help,
Gianluca
-----
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 U
> But now for the most important question: is there a reproducible problem with
> the angle?
Yes. I include everything into a tar:
http://biocroma.unizh.ch/gianluca/Files/Gromacs/hbond.tar.bz2
I'm using the following command to verify if the hydrogen bond "ARG 552
HH12 - GLN 548 OE1" is formed
cumentation:
http://www.gromacs.org/documentation/reference_3.3/online/g_hbond.html
Gianluca
-
Dr. Gianluca Interlandi [EMAIL PROTECTED]
+1 (206) 685 4432
+1 (206) 714 4303
http://biocroma.
n bonds which are merged, and thus
the number of hbonds in "hbond.ndx" would 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 [EM
rary of what 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
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