n)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
>
--
Mala L. Radhakrishnan
Associate Professor of Chemistry
Director, Biochemistry Program
Wellesley College
106 Central Street
Wellesley, MA 02
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Thanks! (and sorry about all the typos in my original email -- just
re-read it and saw it was barely intelligible!)
M
On Thu, Jul 25, 2019 at 4:25 PM Justin Lemkul wrote:
>
>
> On 7/25/19 4:11 PM, Mala L Radhakrishnan wrote:
> > Hi,
> >
> > I am trying to crod sna
hanks!
Mala
--
Mala L. Radhakrishnan
Associate Professor of Chemistry
Director, Biochemistry Program
Wellesley College
106 Central Street
Wellesley, MA 02481
(781)283-2981
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List b
ne but gmx rmsf is finicky and so using the .pdb trajectory,
so long as it works, is fine, and this bug shouldn't indicate an issue with
my .xtc file?
Thanks for any info...
Mala
On Fri, Jul 19, 2019 at 5:28 AM Mala L Radhakrishnan
wrote:
> Hi all,
>
> I am trying to run gmx RMSF u
m using as my reference structure
and made sure that it contains all the atoms in the index file selection
I'm using for my RMSF calculation...
Thanks for any help. I am happy to send you the files for which it works
and for which it doesn't...just very confused!
Mala
--
Mala L. Rad
thank you!
Mala
On Tue, May 28, 2019 at 8:01 AM Justin Lemkul wrote:
>
>
> On 5/28/19 7:49 AM, Mala L Radhakrishnan wrote:
> > Hi all,
> >
> > A quick question -- I just wanted to double check that the Coulomb-SR
> term
> > does NOT include the Coulomb-1
the total Coulombic energy within a
cutoff or switching distance, one would need to ADD the 14 and SR terms.
Is this correct?
Thanks,
M
--
Mala L. Radhakrishnan
Whitehead Associate Professor of Critical Thought
Associate Professor of Chemistry
Wellesley College
106 Central Street
Wellesley, MA
thank you!
On Tue, Apr 9, 2019 at 11:33 AM Justin Lemkul wrote:
>
>
> On 4/1/19 8:21 AM, Mala L Radhakrishnan wrote:
> > Hi all,
> >
> > I wanted to double check something which I believe is true based on doing
> > my own tests, but --
> >
> > W
quot; of a
partner that is solvent-exposed upon binding, I would need to choose the
complex as the group but then output each atom's SASA and then sum over the
atoms in the relevant binding partner. Yes?
Thanks so much!
Mala
--
Mala L. Radhakrishnan
Whitehead Associate Professor of C
ility for the Parallel Reduction on Multi- and
> Many-Core Architectures
>
> https://hal.archives-ouvertes.fr/hal-00949355v4/document
>
> It is unclear if it would be too expensive to implement such methods in
> GROMACs though.
>
> Benson
>
> On 3/22/19 10:11 PM, Mala L
ult for domain decomposition means
> divergence happens by default. After a few ps it's logically equivalent to
> starting from different velocities. See the GROMACS user guide for more
> details on reproducibility questions!
>
> Mark
>
> On Fri., 22 Mar. 2019, 18:15 Mala L
e equilibration (as measure by RMSD) is reached? That's what I'm seeing,
so I wanted to make sure that these differences can actually be this big.
Or is there some other source of stochasticity I'm forgetting?
Thanks so much, and I hope my question makes sense.
M
--
Mala L. Radha
explanation. We will probably put
> out a new 2018 version with that fix next week (or so).
>
> Mark
>
> On Thu., 14 Feb. 2019, 20:26 Mala L Radhakrishnan, >
> wrote:
>
> > Hi all,
> >
> > My student is trying to do a fairly straightforward MD simulation -- a
&g
ode with only a single AVX-512 FMA unit (in which case AVX2 is
faster),
while the node you are running on has dual AVX-512 FMA units.
--
Mala L. Radhakrishnan
Whitehead Associate Professor of Critical Thought
Associate Professor of Chemistry
Wellesley College
106 Central Street
Wellesley, MA 0
ne is
problematic.
M
On Fri, Feb 8, 2019 at 8:32 AM Justin Lemkul wrote:
>
>
> On 2/8/19 8:29 AM, Mala L Radhakrishnan wrote:
> > Hi Justin,
> >
> > Yes, but I don't want anything sticking out of the box. I need the shape
> > of my entire system, when vi
...and molecules at the edges can totally be broken. So really just a
translation of the box coordinates to be centered on the desired group. It
should really be very straighforward.
If it's easier to take offline, I'm happy to.
M
On Fri, Feb 8, 2019 at 8:29 AM Mala L Radhakrish
end?
Mala
On Fri, Feb 8, 2019 at 8:18 AM Justin Lemkul wrote:
>
>
> On 2/8/19 8:15 AM, Mala L Radhakrishnan wrote:
> > Hi Justin,
> >
> > Also -- this is important, I need to maintain the shape of the cubic box,
> > so I do *not* want to keep molecules at the bo
-- just want to make sure before I start making these
huge files :)
Mala
On Fri, Feb 8, 2019 at 8:07 AM Justin Lemkul wrote:
>
>
> On 2/8/19 8:03 AM, Mala L Radhakrishnan wrote:
> > Hi Justin,
> >
> > Thank you SO much -- I will try this out, but I have a silly que
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs
than necessary?
If there is no other way, then I will do it, but these are massive files
and I'd need to create them for many simulations.
Thanks,
M
On Fri, Feb 8, 2019 at 6:56 AM Justin Lemkul wrote:
>
>
> On 2/8/19 6:52 AM, Mala L Radhakrishnan wrote:
> > Hi Paul,
>
dimensions?
>
>
> Peter
>
> On 07-02-19 22:20, Mala L Radhakrishnan wrote:
> > Hi Justin,
> >
> > Thank you -- the good news is that the center of mass of this group does
> in
> > fact match what I calculate to be the COM with my script.
> >
> >
Lemkul wrote:
>
>
> On 2/7/19 1:52 PM, Mala L Radhakrishnan wrote:
> > Hi Justin,
> >
> > I've verified the I'm entering in the right group and that it's correct
> in
> > the index file. Where do I find the output for what it thinks is t
error.
thanks again for instructions on how to get this info..
Mala
On Thu, Feb 7, 2019 at 1:46 PM Justin Lemkul wrote:
>
>
> On 2/7/19 1:36 PM, Mala L Radhakrishnan wrote:
> > Thanks...but these don't really address the issue I have. I've written
> my
> > own scr
m/search?all_words=1&attachments=0&commit=Submit&issues=1&options=0&page=1&q=-center&scope=all&titles_only=&utf8=%E2%9C%93
>
> b) http://redmine.gromacs.org/issues/2579
>
> but not sure if the exactly match what you have.
>
> Benson
>
> On 2/6/
...and as a follow up, it doesn't seem to be centering at either the
geometric center OR the center of mass. Any insight would be appreciated.
Mala
On Wed, Feb 6, 2019 at 10:15 AM Mala L Radhakrishnan
wrote:
> Hi,
>
> It would be helpful to know if this is a known bug/issue.
> Maybe this is known issue..?
>
> Regards,
> Gyorgy
>
> On Tue, 5 Feb 2019 at 20:27, Mala L Radhakrishnan
> wrote:
>
> > Hi again,
> >
> > As a follow up to my earlier email -- I added -pbc atom to the flags,
> for a
> > total command line of:
&
still not centered at the geometric center of the group I chose. I'm not
sure why including -pbc atom would make things different from not including
it in this case, either. Any help would be appreciated.
Mala
On Tue, Feb 5, 2019 at 11:37 AM Mala L Radhakrishnan
wrote:
> Hi,
>
>
place the geometric center of the group you choose
at the geometric center of the box. Am I incorrect? Is there another way
to accomplish what I want?
Thank you so much,
Mala
--
Mala L. Radhakrishnan
Whitehead Associate Professor of Critical Thought
Associate Professor of Chemistry
Wellesley Co
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