Thank you for your clarification.
Rama
On Fri, Sep 17, 2010 at 5:49 PM, Justin A. Lemkul wrote:
>
>
> Ramachandran G wrote:
>
>> Thank you Justin,
>> You are right i am not comparing the same force field.
>> But i am still curious to know the conversion factor for epsilon from
>> MOIL to g
Ramachandran G wrote:
Thank you Justin,
You are right i am not comparing the same force field.
But i am still curious to know the conversion factor for epsilon from
MOIL to gromacs(charmm)force field.
i.e., for sulfur epsilon value of 0.25 to 1.8828. Thank you.
If you are not compa
Thank you Justin,
You are right i am not comparing the same force field.
But i am still curious to know the conversion factor for epsilon from
MOIL to gromacs(charmm)force field.
i.e., for sulfur epsilon value of 0.25 to 1.8828. Thank you.
with regards,
Rama
On Fri, Sep 17, 2010 at 5:21 P
Ramachandran G wrote:
I understood from the gromacs manual the units for epsilon and sigma are
KJ/mol and nm and the corresponding units in MOIL Kcal/mol and Angstom.
But when i checked for some atoms, the epsilon values are not matching.
i.e., for example i took the value of epsilon value o
I understood from the gromacs manual the units for epsilon and sigma are
KJ/mol and nm and the corresponding units in MOIL Kcal/mol and Angstom. But
when i checked for some atoms, the epsilon values are not matching. i.e.,
for example i took the value of epsilon value of S from gromacs 1.8828 and
Krzysztof Kuczera wrote:
Hi GMXers,
I am interested in simulating blocked peptides with CHARMM (and other
force fields), using gromacs-4.5, and would appreciate some help from
more experienced GROMACS users on details.
To test things out I made a stab at creating an ACE N-terminal patch -
t
Hi GMXers,
I am interested in simulating blocked peptides with CHARMM (and other
force fields), using gromacs-4.5, and would appreciate some help from
more experienced GROMACS users on details.
To test things out I made a stab at creating an ACE N-terminal patch -
this exists in OPLSAA, AMBER
Ramachandran G wrote:
Hi gmx-users,
I would like to know the units conversion of epsilon, sigma (from
non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs.
Thank you.
My guess would be that each of the respective manuals would discuss whatever
unit conventions are uti
Hi gmx-users,
I would like to know the units conversion of epsilon, sigma (from
non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs.
Thank you.
with regards,
Rama
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please se
Hi,
Of the "cheap" models I would think tip4p 2001 is the best.
This has been parametrized to reproduce the phase diagram of water
and does surprisingly well.
Berk
> From: vvcha...@gmail.com
> Date: Fri, 17 Sep 2010 16:01:50 -0400
> To: gmx-users@gromacs.org
> Subject: [gmx-users] force field t
Hi all,
Sorry for my a bit off-top message. Does anybody know the force field
model for water (polarizable/non-polarizable) that can reproduce the
temperatures of liquid freezing/evaporation? For other common liquids,
such models are also of interest. Thanks a lot. ~Vitaly
--
Dr. Vitaly V. Chaban
Hi,
I am using g_cluster to analyse a trajectory (protein backbone):
g_cluster -f traj.xtc -s topol.tpr -g cluster.log -skip 10 -cutoff 0.5 -fit
-method linkage
As a result I get almost hundred clusters. The plot of the RMSD against time
for the same trajectory generated with g_rms shows a max
Thanks for the reply.
In fact I had the trajectory with water but then I removed it to have smaller
size of files. the point is that It didn't complain or crash when I was using
that trajectory, choosing water in the groups selecting. but it didn't also
generate any output. that is why I asked t
On 9/17/10 5:37 PM, Justin A. Lemkul wrote:
Fahimeh Baftizadeh Baghal wrote:
hello,
I have a trajectory generated by gromacs in which I excluded water and
there is only protein, now I like to see how does the number of h_bond
between water and protein change during the trajectory. In fact when
Fahimeh Baftizadeh Baghal wrote:
hello,
I have a trajectory generated by gromacs in which I excluded water and
there is only protein, now I like to see how does the number of h_bond
between water and protein change during the trajectory. In fact when I
use g_hbond I can choose the water and
hello,
I have a trajectory generated by gromacs in which I excluded water and
there is only protein, now I like to see how does the number of h_bond
between water and protein change during the trajectory. In fact when I
use g_hbond I can choose the water and protein but I was wondering where
d
gmx-users-requ...@gromacs.org wrote:
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Stacey Meadley wrote:
Hi Justin,
the gromacs version is 4.0.4.
command line: pdb2gmx -f 1B9Eostate.pdb -o 1B9Eostate.gro -p
1B9Eostate.top -ff amber03
message: WARNING: atom H is missing in residue ILE 2 in the pdb file
You might need to add atom H to the hydrogen database of
resi
Hi
It seems that the non-polar energy term has gone missing, and does not get
included in the print-out.
While adding it back again properly I found some other issues that I need to
check before committing. The total potential energy should be correct.
/Per
16 sep 2010 kl. 17:47 skrev "Ehu
Hi Justin,
the gromacs version is 4.0.4.
command line: pdb2gmx -f 1B9Eostate.pdb -o 1B9Eostate.gro -p 1B9Eostate.top
-ff amber03
message: WARNING: atom H is missing in residue ILE 2 in the pdb file
You might need to add atom H to the hydrogen database of residue
ILE
in the file ff
Hi,
I just got a mail from a CHARMM developer saying that charge groups in CHARMM
have no influence on the way forces are calculated.
The details of the use of charge groups in CHARMM are not how I guessed they
were,
but the conclusion is that one should use no charge groups (or single atom
cha
Hi,
I think there is no point in exactly copying the way a certain program treats
things technically,
except for checking force field implementation, but since that can be done
without cut-off's
there no real need.
Charge groups are an ancient leftover from the old times when plain cut-off's
w
Hi Berk and others,
I have been wondering if there was another way to treat the large charge
groups for the CHARMM forcefield(s) in GROMACS, rather than using the
-nochargegrp option.
The reason I ask is because changing every atom to be in individual
charge groups changes the forcefield (al
Have you looked in the ffnabonded.itp and ffnanonbonded.itp? To me it
looks like all of the atom types/bonds/angles are there.
I have just made a very quick rtp entry from the stream file (see
attached) and it seems to work fine (but please do check it). Note the
very large charge groups, so y
Anirban Ghosh wrote:
Hi Justin,
Thanks a lot for the reply.
Yes I have had a look at section 4.4.2. But section 5.3 tells that this
WHAM can be used with the REMD data set as well. So my question is that
how to present this REMD data of multiple trajectories as input to WHAM?
Do I need to w
Hi Gromacs users,
Let me give an idea about what i am doing.
I was doing a Steered Molecular dynamics of ligand transport through
the transporter channel. I want to do the PMF calculation using
Umbrella sampling. I followed the steps provided in the (Justin's)
tutorial. I have generated all configu
Hi all,
Has anybody managed to use ATP with the charmm27 ff in gromacs 4.5? The
forcefield files are missing atom and bond types and angle information.
This is available for charmm, but I have only found it in "stream" file
and have no idea how to convert it. It should be possible (for someone
Hi,
The choice of charge is significant even with PME, because of the way
Gromacs makes the neighborlists.
As I mailed before, use the -nochargegrp option of pdb2gmx with the Charmm27 ff.
Berk
> Date: Fri, 17 Sep 2010 11:46:36 +0200
> From: qia...@gmail.com
> To: gmx-users@gromacs.org
> Subjec
You should change the charge group number. Every charge group include
several, like 3-4, atoms. Actually, the definition of charge group is
not significant if you use PME for the coulomb interaction.
nahren manuel wrote:
> Dear Gromacs Users,
>
> I am using plain cutoff for my 12-mer protein.
>
Hi,
No, you should never change the charges in a force field!
Run pdb2gmx again with the -nochargegrp option.
That will make the size of all charge groups a single atom.
This will be done automatically in the 4.5.2 release which will be out soon.
Berk
Date: Fri, 17 Sep 2010 02:32:31 -0700
From
Dear Gromacs Users,
I am using plain cutoff for my 12-mer protein.
The grompp reports ARG to have a big charge group. this was also highlighted in
the following mail
http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html
I was just think if changing the charges on these atoms would help
Hi,
For position restraints there is an mdp option refcoord_scaling that sets how
the reference positions are affected by pressure scaling.
Berk
> Date: Thu, 16 Sep 2010 21:15:38 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] about NPT run
>
>
>
> zhongj
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