On Wed, Jun 23, 2010 at 10:20:19AM +0100, Kukol, Andreas wrote:
> Yes, that is an interesting question. I don't know the answer, but is there
> any way to get the numerical values of the matrix from Gromacs tools that
> produce a matrix in xpm format ? I have problems with g_rms and g_rmsdist is
On Tue, Sep 29, 2009 at 07:00:55PM +0530, ram bio wrote:
> Dear Gromacs users,
>
> I have a modelled protein whose net charge is +12.69, and I would like to
excellent. now you neutralize it by adding 12 Cl- ions, and then
check the periodic table for an ion that has a charge of -0.69.
if you ca
I'm trying to do a cvs update on the 3.3 patches branch, but get a
connection time out on cvs.gromacs.org
is there any way I can resolve this?
(I need to do the update because of the following:
gmx_disre.c: In function 'gmx_disre':
gmx_disre.c:601: error: too few arguments to
On Wed, Jun 17, 2009 at 06:57:24AM -0400, Justin A. Lemkul wrote:
>
> The .mdp file seems reasonable. QM charges are not necessarily the end
> result in Gromos parameterization. In fact, such calculations are often
> unnecessary. In my experience, assigning charges based on functional groups
>
new) parameterization needs to be verified and
validated!
cheers,
marc
--
Marc F. Lensink (Ph.D.)
Structure and Function of Biological MembranesSFMB
Centre for Structural Biology and Bioinformatics CSBB
Université Libre de Bruxelles (ULB) marc.lens...@ulb.ac.be
Boulevard d
On Tue, Mar 31, 2009 at 07:23:57AM -0400, Justin A. Lemkul wrote:
>
> Force fields have to be internally self-consistent, so using the parameters
> from OPLS with Berger lipids will give spurious results. The only proper
> combinations are Gromos/Berger or OPLS/converted Berger.
as long as one
real work.
I can confirm that. I've used inflategro recently with POPE. in one
case no problems, in another I indeed solved it by decreasing the
charges.
cheers,
marc
--
Marc F. Lensink (Ph.D.)
Structure and Function of Biological MembranesSFMB
Centre for Structural Biology an
On Thu, Feb 19, 2009 at 01:56:28AM +1100, Mark Abraham wrote:
> Chao Zhang wrote:
> >Hi Mark,
> >
> >I think 3.3.2, does it be fixed in 4.0?
>
> I don't know - I've not seen it reported. You should search the mailing
> list archives.
I've solvated with tip4p in 3.3cvs and 3.3.1, never had the pr
On Wed, Jan 07, 2009 at 09:43:25AM +1100, Mark Abraham wrote:
> jayant james wrote:
> >Hi!
> >I have been performing MD simulations of a protein which has 3 ca2+
> >ions. I find that after 3ns of simulations the ca2+ ions start to drift
> >away. So what would be a good strategy to have the ca2+ i
On Thu, Nov 06, 2008 at 04:13:04PM +0530, Bhawana Gupta wrote:
> thanks for reply.
> but sir, when i start it with 1ns md simulation,my peptide doesnot get
> stable because it was moving in zigzag like motion.
> so should i go for 5 ns or not.
> which ns means (1ns or 2ns...20ns) is better so t
ct
balance between 1) too short simulations have no biological relevance
and 2) too long simulations deviate too much from reality because of
imperfect parameters. so 3) always compare/compliment with experiment
(if possible).
cheers,
marc
--
Marc F. Lensink
Centre for Structural Biology
On Wed, Oct 29, 2008 at 01:33:19PM +0200, Inon Sharony wrote:
> Hello GROMACS users & team
>
> I would like to run grompp and mdrun from the command line without
> having to see all the possible flags and options. I'm running a few
> commands in series, so I can't use "grompp &" and then "mdru
Large
probe?
cheers,
marc
--
Marc F. Lensink
Centre for Structural Biology and Bioinformatics CSBB
Université Libre de Bruxelles [EMAIL PROTECTED]
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
tel: +32 2 650 5411 secr: +32 2 65
On Sat, Sep 27, 2008 at 03:05:55PM -, minnale wrote:
>
> Hi all
> My system was crashed inbetween simulation, so restarted the run by using
> tpbconv command
> tpbconv -f popc.trr -e popc.edr -s popc.tpr -o popc_restart -time 2235.2
> -until 3000 it showing
>
> Last frame read 6173
pid with proper area per lipid. alternatively you could
use isotropic pressure coupling and hope that the referees don't mind,
or apply a positive surface tension like the charmm people.
cheers,
marc
--
Marc F. Lensink
Centre for Structural Biology and Bioinformatics CSBB
Univ
tinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
be requests
> >>to the
> >>>>>
> >>>> list. Use the
> >>>>
> >>>>> www interface or send it to
> >>>>>
> >>>> [EMAIL PROTECTED]
> >>>>
> >>&g
xperience with tip5p and membranes
with us, that would be great. some time ago i decided to switch to
all-atom simulations, and then had to make the choice between tip4p
and tip5p. now for the life of me i don't remember *why*, but i do
know that there were some strong arguments against tip5
id
phase, it's probably not what you want. personally i'm not (yet)
convinced it's a better combination than berger/gromos/spc, though.
cheers,
marc
--
Marc F. Lensink
Centre for Structural Biology and Bioinformatics CSBB
Université Libre de Bruxelles [EMAIL PROTE
teep energy well with
wide barriers so that the assignment of new velocities also doesn't
work. if the system is constructed from a previous simulation, find a
few time frames before and re-construct. otherwise i suppose you
could identify the faulty atom and delete the nearest water molec
ge z position of the phosphorus atoms of both
layers, then remove all water molecules - of the just added set! -
that lie in between.
cheers,
marc
--
Marc F. Lensink
Centre for Structural Biology and Bioinformatics SCMBB
Université Libre de Bruxelles [EMAIL PROTECTED]
Boulevard du Tr
On Mon, Oct 29, 2007 at 09:54:08AM +0100, David van der Spoel wrote:
> Marc F. Lensink wrote:
> >On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote:
> >>Anupam Nath Jha wrote:
> >>>Dear all
> >>>can i calculate the angle between trans-mem
On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote:
> Anupam Nath Jha wrote:
> >Dear all
> >can i calculate the angle between trans-membrane alpha-helices by using
> >gromacs?
>
> Probably. Check out section 7.4 of the manual.
i wrote a program for that. contact me off-list.
as soon
On Wed, Jun 20, 2007 at 07:27:42AM -0700, priyanka srivastava wrote:
> Dear All,
>
> I want to calculate tilt angle of a peptide inserted
> inside the lipid bilayer (i.e. angle between the
> helical axis and bilayer normal). From previous posts
> I got an idea that g_bundle wud solve my problem.
On Wed, May 16, 2007 at 05:16:49PM -0700, David Mobley wrote:
> >So what you really need to do, once you have worked out which forcfield
> >you are going to use, go back to the documentation / papers for that
> >particular forcefield, see how they generated the parameters, then use
> >that same pro
On Tue, Apr 03, 2007 at 10:16:12AM -0400, Chris Neale wrote:
> Thanks for the reply. Are you sure that it is there? I checked that
> prior to sending the fist request and I checked it again now. Ordered by
> date, the most recent entry is "StressCPU, version 2.0 09.02.2007" and
> next is "g_spat
On Sun, Mar 11, 2007 at 05:16:04PM +1100, Mark Abraham wrote:
> Marc F. Lensink wrote:
> >hi tom,
> >
> >>the pdb2gmx is unable to convert a peptide bound to a protein because it
> >>does not recognise the PTR (phosphotyrosine) in the peptide. Gromacs
> >
hi tom,
> the pdb2gmx is unable to convert a peptide bound to a protein because it does
> not recognise the PTR (phosphotyrosine) in the peptide. Gromacs manual says
> that you can only resolved this
> by changing the adding the residue to the rtp files. The problem now is that
> I do not hav
On Fri, Jan 12, 2007 at 04:08:47PM +0100, Luca Mollica wrote:
> Dear GMX users,
>
> I am trying to simulate a post translational modification of a protein,
> actually a glutathionylation of a Cys. I have tried a couple of times to
> create a disulphide bridge between two Cys and I managed to do
and its x, y and z
components are plotted. This other group can have its atoms that make part of
the UNDER group excluded when -not is given. If -coord is supplied, also the
individual centre-of-mass coordinates of the two groups are plotted.
cheer
ieve. So does anyone know of any gromacs stuff
> using negative lipids, or alternatively a reason why
> this hasn't been done?
i have done simulations with mixed bilayers, containing popc and a
fraction of popg, pops, or popa. i cannot imagine being the only one
to have done that.
cheers
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