t;
> Hope it helps,
>
> Tsjerk
>
> On Mar 25, 2010 7:22 PM, "Joe Joe" wrote:
>
> I am seeing weird behavior when I trjconv my trajectory containing NaCl,
> tip3p, and protein. I use the OPLSAA force field and octahedral PBCs.
>
> When I run
>
> trjconv -f
I am seeing weird behavior when I trjconv my trajectory containing NaCl,
tip3p, and protein. I use the OPLSAA force field and octahedral PBCs.
When I run
trjconv -f traj.trr -s topol.tpr -pbc nojump -o trajout.xtc
The ions in the output form clusters of three similarly charged ions in the
shaped
I think there is a tdb problem when using pdb2gmx on a single amino acid.
The tdb databases replaces the CA with different charges depending on
whether its a c or n termini. When its a single amino acid you get the c
terminal charge and thus the overall charge is incorrect. Am I missing
something?
ory. You can also copy it to your
> working directory and change it there, as it will then take precedence
> over the other one. Do mind to increment the number at the top of the
> file for every amino acid you add.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Mar 12, 2010 a
How do I tell pdb2gmx what the termini are in my molecule. I added a non
standard amino acid to the ffoplsaa.rtp database but pdb2gmx says "No N- or
C-terminus found: this chain appears to contain no protein".
thanks,
Ilya
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.o
Bruce,
This is great. I was able to easily make a molecule that runs with OPLS-AA.
Would it be possible to add a feature which creates an *.rtp entry? It would
be really useful for making non standard amino acids and incorporating it
with pdb2gmx.
Thanks,
Ilya
On Wed, Mar 10, 2010 at 11:07 AM,
-09 20.01, Joe Joe wrote:
>
>> I also just tried on a different ALA and got the same problem.
>>
>
> can you please submit a bugzilla and upload files to reproduce the problem?
>
>
>> Ilya
>>
>>
>> On Tue, Mar 9, 2010 at 10:58 AM, Joe Joe > <mail
done, bug #402
On Tue, Mar 9, 2010 at 11:44 AM, David van der Spoel
wrote:
> On 2010-03-09 20.01, Joe Joe wrote:
>
>> I also just tried on a different ALA and got the same problem.
>>
>
> can you please submit a bugzilla and upload files to reproduce the problem?
>
>
I also just tried on a different ALA and got the same problem.
Ilya
On Tue, Mar 9, 2010 at 10:58 AM, Joe Joe wrote:
> I am looking the the gmxdump output and everything seems consistent. The
> only difference is that the numbering in the index file starts at 1 whereas
> in the gm
I am looking the the gmxdump output and everything seems consistent. The
only difference is that the numbering in the index file starts at 1 whereas
in the gmxdump the arrays are indexed starting at 0. The coordinates look
just fine.
Thanks,
Ilya
On Tue, Mar 9, 2010 at 10:30 AM, Joe Joe
On Tue, Mar 9, 2010 at 10:22 AM, David van der Spoel
wrote:
> On 2010-03-09 19.16, Joe Joe wrote:
>
>> yep.
>>
> Have you gmxdump/ed the xtc to check the coordinates are right?
>
>>
>> On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
>> mailto:sp...@x
Hi I am trying to post process and xtc trajectory using g_dist. I am trying
to calculate the CA-CB distance of an Alanine residue but I get NAN in all
the distance columns. It works for the other residues I've tried (i.e. SER,
VAL). I am using vsites in my simulation and I think it may have some th
yep.
On Tue, Mar 9, 2010 at 10:15 AM, David van der Spoel
wrote:
> On 2010-03-09 19.09, Joe Joe wrote:
>
>> Hi I am trying to post process and xtc trajectory using g_dist. I am
>> trying to calculate the CA-CB distance of an Alanine residue but I get
>> NAN in all the di
Hi I am trying to post process and xtc trajectory using g_dist. I am trying
to calculate the CA-CB distance of an Alanine residue but I get NAN in all
the distance columns. It works for the other residues I've tried (i.e. SER,
VAL). I am using vsites in my simulation and I think it may have some th
Will do thanks.
Ilya
On Sun, Apr 12, 2009 at 7:50 PM, Mark Abraham wrote:
> Joe Joe wrote:
>
>> It works just fine without RE.
>>
>
> OK well that sounds like after a replica exchange attempt, some data
> structure isn't being (re-)constructed correctly. See if yo
It works just fine without RE.
On Sat, Apr 11, 2009 at 8:49 PM, Mark Abraham wrote:
> Joe Joe wrote:
>
>> Hi Justin,
>>
>> Thanks for helping me with this.
>> On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>
On Sat, Apr 11, 2009 at 8:13 PM, Justin A. Lemkul wrote:
>
>
> Joe Joe wrote:
>
>> Hi Justin,
>>
>> Thanks for helping me with this.
>> On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>
Hi Justin,
Thanks for helping me with this.
On Sat, Apr 11, 2009 at 4:46 AM, Justin A. Lemkul wrote:
>
>
> Joe Joe wrote:
>
>> How do I determine what those values should be? How does it affect the
>> simulation?
>>
>>
> The header of your log file shoul
How do I determine what those values should be? How does it affect the
simulation?
thanks,
Ilya
On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul wrote:
>
>
> Joe Joe wrote:
>
>> Hi All,
>>
>> I get the following error when running replica exchange. I have 32
Hi All,
I get the following error when running replica exchange. I have 32 replica's
with each replica running on 4 processors (128 total). How do I decrease the
domain decomposition cell size, -dss? What should I set it to?
Thanks,
Ilya
DD cell 2 0 0: Neighboring cells do not have atoms: 22217
I finally figured it out. I went through every parameter step by step and it
turns our I had epsilon-r set to 80. Not sure why I had that. Wish gromacs
would have given me a warning (hint hint). That explains why my P.E. was
10^-5 instead of 10^-6. Thanks everyone for trying!!!. Sometime the most
o
Nope not an A/nm problem.
As a simple test I take spc.gro from share/top.
I reconfigure the box (i.e. editconf -f spc.gro -d 1.0 -c -bt cubic -o
water_center.
I then solvate with genbox, minimize and run using the mdp file I provided
earlier.
No matter how much minimization I do the volume of the
On Thu, Apr 9, 2009 at 6:36 AM, Justin A. Lemkul wrote:
>
>
> Joe Joe wrote:
>
>> So I got my small water box (800 waters) to behave stably with pressure
>> coupling after more minimization but I still can't get my large system to
>> work with pressure cou
What about use for commercial purposes?
On Thu, Apr 9, 2009 at 1:31 AM, FyD wrote:
> Dear All,
>
> I am pleased to announce the release of R.E.D. Server available @
> http://q4md-forcefieldtools.org/REDS/.
>
> R.E.D. Server provides the software and hardware (i. e. a cluster of
> computers) requ
t) and for all terms an amplitude (real)
; and a phase angle (real)
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
On Wed, Apr 8, 2009 at 1:00 PM, Joe Joe wrote:
>
>
> On
On Wed, Apr 8, 2009 at 11:31 AM, Roland Schulz wrote:
>
>
> On Wed, Apr 8, 2009 at 7:53 AM, Joe Joe wrote:
>
>> HI Chris,
>>
>> On Tue, Apr 7, 2009 at 9:31 PM, wrote:
>>
>>> Hi Ilya,
>>>
>>> First thing that comes to mind is that
I tried .1, and 10 ps tau_p values. I guess I can try smaller values.
On Wed, Apr 8, 2009 at 10:44 AM, Justin A. Lemkul wrote:
>
>
> Joe Joe wrote:
>
>> Hi Chris,
>>
>> When I create the topology for the 4fs timestep I use pdb2gmx -vsite h. I
>> set up the
Yeah I only gave a partial. Tried to remove the QM params. I do use
constraints = all-bonds.
On Wed, Apr 8, 2009 at 9:18 AM, wrote:
> You say "I run all he sims with constraints=all-bonds", but I don't see
> that in the mdp options that you provided. I even put your text in a file
> and grepped
Hi Chris,
When I create the topology for the 4fs timestep I use pdb2gmx -vsite h. I
set up the correct constraints. I've tested it and it conserves energy in
NVE. I run all he sims with constraints=all-bonds. I am now running a single
water box (800 water molecules) with 1s time steps and the volum
HI Chris,
On Tue, Apr 7, 2009 at 9:31 PM, wrote:
> Hi Ilya,
>
> First thing that comes to mind is that it is strange to couple a coulombic
> switching function with PME. While this could possibly be done correctly, I
> doubt that it is in fact done in the way that you expect (i.e. correctly) in
Hi
I am having some pressure coupling issues. I have a fairly large
protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I
run NVE it conserves energy with appropriate parameter settings. If I run
NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
Rahman), the s
Conservation with 4fs timestep
> >
> > Joe Joe wrote:
> > > Hi,
> > >
> > > I get good conservation when running NVE in gromacs with 4 fs when I
> use
> > > PME-switch for electrostatics but not so good when I use switch. Any
> > > thought
Hi,
I get good conservation when running NVE in gromacs with 4 fs when I use
PME-switch for electrostatics but not so good when I use switch. Any
thoughts why that would be? Params shown below.
Thanks,
Ilya
;
; File 'mdout.mdp' was generated
; By user: ichorny (502)
; On host:
On Mon, Mar 30, 2009 at 3:23 PM, Joshua Adelman wrote:
> I am interested in potentially using gromacs to do some calculations on an
> C-alpha based elastic network model of the protein that I'm working on. I'm
> curious if other users have done similar types of calculations, and if so,
> what prot
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