Dear Gromacs users,
I am planing to use wildcard atomtypes in [
dihedrals ] directive of the ffbonded.itp file, As my system contain O-C
dihedral, all the O-C dihedrals are same, so instead of mentioning each
dihedral explicitly i have tried wildcard atom types by
On 2012-05-04 00:37, Dallas Warren wrote:
Did you plot the box volume, box dimensions or density with simulation time?
Over those 500,000 steps it should be shrinking.
It would also be a good idea if you made a box size and number of molecules
that is at least close to the density of octanol.
On Thu, 2012-05-03 at 18:43 +0200, Patrick Fuchs wrote:
> Hi Florian,
>
> >> I remark that Langevin method is used also for explicit water system!
> >
> > But there a big question arises to me. The thermostatting by Langevin is
> > achieved due to random kicks. If I simulate all atoms explicitly,
4 maj 2012 kl. 10.45 skrev Dommert Florian:
> On Thu, 2012-05-03 at 18:43 +0200, Patrick Fuchs wrote:
>> Hi Florian,
>>
I remark that Langevin method is used also for explicit water system!
>>>
>>> But there a big question arises to me. The thermostatting by Langevin is
>>> achieved due t
Hi there,
look at 'acpype -h', in particular:
-g, --disambiguatedisambiguate lower and uppercase atomtypes in GMX top
file
Alan
On 3 May 2012 14:34, Vedat Durmaz wrote:
>
> hi guys,
>
> i'm trying to simulate some receptor ligand system with implicit solvent
> usi
On Fri, 2012-05-04 at 11:07 +0200, Erik Marklund wrote:
>
> 4 maj 2012 kl. 10.45 skrev Dommert Florian:
>
> > On Thu, 2012-05-03 at 18:43 +0200, Patrick Fuchs wrote:
> > > Hi Florian,
> > >
> > > > > I remark that Langevin method is used also for explicit water
> > > > > system!
> > > >
> > >
Gromacs? نقاشی؟ :)
On 5/2/12, leila separdar wrote:
> salam,
> man mishnasametun?
> mozoe naghashie chiye?
>
> 2012/5/2 Shima Arasteh
>
>>
>> سلام
>> یه خواهش دارم. من بعد قاب کردن نقاشی، ازش عکس نگرفتم. لطفا اگر تونستین
>> برام چندتا عکس خوب بگیرین
>> مرسی
>> میشه لطفا؟
>>
>>
>>
>> --
>> gmx-u
Salam,
man yekam Farsi fahmam, amma only in Penglish ;) However, perhaps you
try English and get more response.
Khodafes,
Flo
On Fri, 2012-05-04 at 04:50 -0700, Hengameh Fallah wrote:
> Gromacs? نقاشی؟ :)
>
> On 5/2/12, leila separdar wrote:
> > salam,
> > man mishnasametun?
> > mozoe naghas
thanks justin and alan.
i also had the suspicion that the error is caused by case sensitivity.
simply replacing all atom types from lower to upper case within the
ligand.itp file yields the same error: "missing gb parameters".
using the "--disambiguate" option for the parameterization with
On 5/4/12 9:14 AM, Vedat Durmaz wrote:
thanks justin and alan.
i also had the suspicion that the error is caused by case sensitivity. simply
replacing all atom types from lower to upper case within the ligand.itp file
yields the same error: "missing gb parameters".
using the "--disambiguate
Hi, all, I'm still confused about how to set up 1-4 interaction tables
for tabulated non-bonding potentials when using the -tablep option in
mdrun.
The specific question is:
How must I specify the 1-4 interaction in those tables? How many
columns? What to put in these columns?
My primary goal is t
yes, i do understand this. but what i really do not get is that grompp
fails telling me "GB parameter(s) missing or negative for atom type
'C'", ALTHOUGH 'C' is listed in gbsa.itp.
thus, from 15 atom types reportedly lacking gb parameters according to
grompp, about 10 ARE listed in gbsa.itp.
On 5/4/12 9:44 AM, Vedat Durmaz wrote:
yes, i do understand this. but what i really do not get is that grompp fails
telling me "GB parameter(s) missing or negative for atom type 'C'", ALTHOUGH 'C'
is listed in gbsa.itp.
thus, from 15 atom types reportedly lacking gb parameters according to gr
Have a look at http://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs
There there's a note:
*NB(1):* #include "Ligand.itp" has to be inserted right after
ffamber**.itp line
and before Protein_*.itp line in *Complex.top*.
Are you inserting your gbsa.itp in the *right* place of your top file?
Dear gmx users,
Why CHARMM27 is a suitable force field for studying ion channels in membrane?
How can I choose the best force field in this field?
Thanks in advance,
Shima
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the arc
Dear Gromacs users
I am currently preparing an RTP file to describe a polymer for use with MARTINI.
MARTINI does not include default bonded interactions, so all bonds,
angles and dihedrals must be explicitly defined in the topology file
or, in my case, in the RTP file.
The problem is that pdb2gm
On 5/4/12 10:22 AM, Shima Arasteh wrote:
Dear gmx users,
Why CHARMM27 is a suitable force field for studying ion channels in membrane?
It describes both protein and lipids quite well, though from what I understand
about CHARMM36, it is probably an even better choice.
How can I choose the
the order of force field, ligand, target is correct. and usually works
fine in explicit solvent simulations.
but i actually do not include the gbsa.itp, since it is defined by the
choice of the force field. (as soon as i rename its gbst.itp, grompp
says it cannot find that file ..)
but in
Hi all,
This week Nvidia has also announced the GeForce GTX 690 with two
Kepler Chips [1].
That will make a total of 3072 CUDA cores @ 915MHz to 1019MHz and will
perform like two GTX 680s in SLI mode [2], but more energy efficient.
I'd really be interested if parallelization would be a bottleneck
Hi
Im trying to calculate the hydration free energy for the molecule Aniline
And I get a free energy value about 10 kcal higher than the experimental value
What I do is I couple vdw then charges from a dummy state and add the two delta
G values using the g_bar method. If you have any idea why is
On 5/4/12 3:56 PM, Milinda Samaraweera wrote:
Hi
Im trying to calculate the hydration free energy for the molecule Aniline
And I get a free energy value about 10 kcal higher than the experimental value
What I do is I couple vdw then charges from a dummy state and add the two delta
G values usi
On Wed, Apr 25, 2012 at 9:38 AM, Szilárd Páll wrote:
> On Wed, Apr 25, 2012 at 11:43 AM, SebastianWaltz
> wrote:
> > Dear all,
> >
> > will the new version 4.6 work together with CUDA 4.2? Would be good to
> > know, since this is needed for the new NVIDIA Gemini cards with Kepler
> > technology.
Please keep all correspondence on the gmx-users list. I am not a private tutor
and you have better odds of solving your problem by allowing others to provide
input.
On 5/4/12 8:01 PM, Milinda Samaraweera wrote:
Hi Justin
Im a very new to using Gromacs. I tried to reproduce the values in sh
On 5/05/2012 1:47 AM, Elton Carvalho wrote:
Dear Gromacs users
I am currently preparing an RTP file to describe a polymer for use with MARTINI.
MARTINI does not include default bonded interactions, so all bonds,
angles and dihedrals must be explicitly defined in the topology file
or, in my case
Hi Gromacs friends,
I completed the justin lipid tutorials upto the three steps ...
While performing the tutorial of lipid written by justin ,
I get following query..
1. As per the tutorials we added the
DPPC chain topology
*; Include DPPC chain topology
#include "dppc.itp"
*
dppc.itp file
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