Dear Justin,
sorry for the late answer and acknowledgements... Please see below my
comments.
Anna
__
Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Giovanni Paolo II, 132
84084 Fisciano (SA)
Hi Pratibha,
The table is all garbled, and your description insufficiently clear for us
to form a mental picture of what you want, what you've tried to get that,
where it goes wrong, or where you get stuck, and how we can help you on the
right track again.
Cheers,
Tsjerk
On Fri, Sep 27, 2013
On 9/27/13 8:18 AM, Anna Marabotti wrote:
Dear Justin,
sorry for the late answer and acknowledgements... Please see below my
comments.
Anna
__
Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via
On 26 Sep, 2013, at 19:50, Justin Lemkul wrote:
On 9/26/13 10:47 PM, Christopher Neale wrote:
Dear Karthi:
As far as I am aware, there is no OPLSAA lipid force field. I have used
Berger lipids with OPLSAA protein
( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is
Hello Gromacs users,
I am the beginner in Gromacs. I want to simulate ionomer in water. I could not
find a pdb file for my case, and I tried to draw the ionomer in Avogadro
software and generated the pdb file. However, gmx cannot find my residue names.
I added my residue name to
On 9/27/13 2:34 PM, Ehsan Sadeghi wrote:
Hello Gromacs users,
I am the beginner in Gromacs. I want to simulate ionomer in water. I could
not find a pdb file for my case, and I tried to draw the ionomer in Avogadro
software and generated the pdb file. However, gmx cannot find my residue
names.
Many thanks Justin.
Here is my .pdb file:
ATOM 1 C LIG 1 -10.450 5.214 -1.717 1.00 0.00 C
ATOM 2 C LIG 1 -8.424 5.477 -1.030 1.00 0.00 C
ATOM 3 C LIG 1 -6.603 5.864 -0.166 1.00 0.00 C
ATOM 4
On 9/27/13 3:17 PM, Ehsan Sadeghi wrote:
Many thanks Justin.
Here is my .pdb file:
ATOM 1 C LIG 1 -10.450 5.214 -1.717 1.00 0.00 C
ATOM 2 C LIG 1 -8.424 5.477 -1.030 1.00 0.00 C
ATOM 3 C LIG 1 -6.603 5.864
Hi,
I just added this to the existing .rtp file in gromos
[ LIG ]
[ atoms ]
C C 0.000 0
F F 0.000 0
[ SCH ]
[ atoms ]
OOM 0.000 0
C C 0.000 0
O O 0.000 0
F F 0.000 0
S S 0.000 0
H
On 9/27/13 4:18 PM, Ehsan Sadeghi wrote:
Hi,
I just added this to the existing .rtp file in gromos
[ LIG ]
[ atoms ]
C C 0.000 0
F F 0.000 0
[ SCH ]
[ atoms ]
OOM 0.000 0
C C 0.000 0
O O 0.000 0
F
Thanks Chris.
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Christopher Neale
Sent: Thursday, September 26, 2013 7:47 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Membrane simulation with OPLS ff.
Dear Karthi:
As far as
Thanks Justin.
I try to modify my file based on your comments.
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Friday, September 27, 2013 1:24:44 PM
Subject: Re: [gmx-users] ionomer topolgy
On 9/27/13 4:18 PM,
Thanks Justin.
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Justin Lemkul
Sent: Thursday, September 26, 2013 7:51 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Membrane simulation with OPLS ff.
On
Hello,
I revised my pdb and rtp files. I still receive similar error message.
Here are the new files:
.pdb:
ATOM 1 C1LIG 1 -10.450 5.214 -1.717 1.00 0.00
C
ATOM 2 C2LIG 1 -8.424 5.477 -1.030 1.00 0.00
C
ATOM 3 C3
On 9/27/13 5:53 PM, Ehsan Sadeghi wrote:
Hello,
I revised my pdb and rtp files. I still receive similar error message.
Whatever modifications you're making probably aren't being done in the right
files. You haven't yet responded to my question about which force field you're
using and
Thanks for your prompt response. I made the modifications on the aminoacids.rtp
file in Gromacs/gromacs-4.6.3/share/top/gromos53a6.ff.
I did not modify any force field. I thought I still can use the default force
field in gromos; isn't it right?
Here is the output from pdb2gmx. Thank you for
On 9/27/13 8:43 PM, Ehsan Sadeghi wrote:
Thanks for your prompt response. I made the modifications on the aminoacids.rtp
file in Gromacs/gromacs-4.6.3/share/top/gromos53a6.ff.
I did not modify any force field. I thought I still can use the default force
field in gromos; isn't it right?
Dear Chris,
Thank you for your reply. I defined a new virtual atomtype (type D) with
LJ sigma 1.72A ( 2*0.7+1.72=3.12, which is sigma of the oxygen) and
played a bit with epsilon till the new LJ repulsion was able to prevent
the build up of a huge force on the oxygen while interacting with
Dear Gmx Users,
I have my carbon nanotube and I wish to make it infinite in lenght. Which
mdp options whall be used? pbc = xy and z is the infinite dimension?
another issue: Would you apply bonds between carbon atoms within the
nanotube or constraints using LINCS? Which of them is less
I think this is in topology, not in MDP. With PBC, you just specify
what happens to the particle after it crosses the edge of the box in
certain direction.
I have no preference regarding LINCS vs harmonic bonds.
You can also freeze only the rim atoms of the nanotube from both
ends and this will
Dear all,
I have a basic doubt. Is there any difference between the two processes
where
1) I concatenate the trajectories and do trjconv to remove PBC, which is a
default process
2) Do trjconv on all the xtc files separately and then concatenate them.
Thank you for your time
--
With Best Wishes
I do not think that I ever tried myself, but is seems all the same.
Why do you ask?
Dr. Vitaly V. Chaban
On Thu, Sep 26, 2013 at 3:40 PM, Venkat Reddy venkat...@gmail.com wrote:
Dear all,
I have a basic doubt. Is there any difference between the two processes
where
1) I concatenate the
On 9/26/13 8:39 AM, Steven Neumann wrote:
Dear Gmx Users,
I have my carbon nanotube and I wish to make it infinite in lenght. Which
mdp options whall be used? pbc = xy and z is the infinite dimension?
another issue: Would you apply bonds between carbon atoms within the
nanotube or constraints
I am just curious why the system would explode without
periodic_molecules = yes. If the PBC procedure is applied before
harmonic bond potential is calculated, than the opposite nanotube
atoms should be (already) seen as neighboring. This looks the same as
the solvent molecule, one atom of which
Hi guys,
Is it possible to specify in the topol.top file preprocessor statements, so
that you can stop the simulation prematurely?
I pull two molecules together and I'd like to stop the simulation if the
center of mass distance of the molecules is less than xx nm.
Best,
grita
--
View this
Unlikely possible... But yeah, the feature might be handy.
Dr. Vitaly V. Chaban
On Thu, Sep 26, 2013 at 4:20 PM, grita cemilyi...@arcor.de wrote:
Hi guys,
Is it possible to specify in the topol.top file preprocessor statements, so
that you can stop the simulation prematurely?
I pull two
Thank you for this. And also I wish to attach a chain to my nanotube so
they will be both able to move together. Is that a matter of distance
restraints between nanotube atom and first atom of my chain or again -
LINCS? Both chain and nanotube are made of the same type of 8 type of
atoms. Please,
No, there's no way to do that. But you can monitor the output
trajectory file yourself, live.
Mark
On Thu, Sep 26, 2013 at 4:49 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
Unlikely possible... But yeah, the feature might be handy.
Dr. Vitaly V. Chaban
On Thu, Sep 26, 2013 at 4:20 PM,
Dear Sir,
Thanks for the quick reply.
I accidentally lost one of my raw .xtc files. But I have the noPBC xtc
file. So, when ever I extend my simulation, first I am removing PBC then
concatenating it with existing noPBC xtc file. Is it fine??
On Thu, Sep 26, 2013 at 7:13 PM, Dr. Vitaly Chaban
Hi Venkat,
It depends on what you mean with removing pbc.
Cheers,
Tsjerk
On Sep 26, 2013 5:21 PM, Venkat Reddy venkat...@gmail.com wrote:
Dear Sir,
Thanks for the quick reply.
I accidentally lost one of my raw .xtc files. But I have the noPBC xtc
file. So, when ever I extend my simulation,
Steven -
I would use a simple harmonic bond.
Dr. Vitaly V. Chaban
On Thu, Sep 26, 2013 at 5:12 PM, Steven Neumann s.neuman...@gmail.com wrote:
Thank you for this. And also I wish to attach a chain to my nanotube so they
will be both able to move together. Is that a matter of distance
Hi
when calculating an energy contribution using g_energy, the units
specified in the plots, as well as in the output tables, are kJ/mol.
This happens even when the -nmol flag is missing (so nmol=1). On the
other hand, the energy units in gromacs are kJ/mol. So I guess that when
a term (a dihedral
Dear users,
For some analysis I require the 27 periodic images
of the system I ran the simulation for. Kindly let me
know how can it be written to a pdb file.
Thanking you
Regards
Kavya
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
*
Dear Tsjerk sir,
I used trjconv -pbc mol -ur compact options.
On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Venkat,
It depends on what you mean with removing pbc.
Cheers,
Tsjerk
On Sep 26, 2013 5:21 PM, Venkat Reddy venkat...@gmail.com wrote:
Dear
Hi Venkat,
These options are 'frame intrinsic' or 'history independent', unlike -pbc
nojump.
Cheers,
Tsjerk
On Sep 26, 2013 6:46 PM, Venkat Reddy venkat...@gmail.com wrote:
Dear Tsjerk sir,
I used trjconv -pbc mol -ur compact options.
On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar
Dear Users:
Has anyone successfully run the free energy tutorial at
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy
?
I just tried it and I get a segmentation fault immediately (see output at the
end of this post).
I get a segfault with both 4.6.3
Hi Kavya,
genconf -nbox 3 3 3
Cheers,
Tsjerk
On Thu, Sep 26, 2013 at 6:24 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
For some analysis I require the 27 periodic images
of the system I ran the simulation for. Kindly let me
know how can it be written to a pdb file.
Thanking
Hi Ángel,
kJ per mol of system contained in the unit cell?
Exactly. As if whatever is in there is one 'molecule' (-nmol 1).
Adios!
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search
On 9/26/13 12:05 PM, Dr. Vitaly Chaban wrote:
Steven -
I would use a simple harmonic bond.
Note that either in the case of the distance restraint or harmonic interaction
approach, both the CNT and the molecule to which it is tethered need to be in
the same [moleculetype], so run pdb2gmx
On 9/26/13 10:19 AM, Dr. Vitaly Chaban wrote:
I am just curious why the system would explode without
periodic_molecules = yes. If the PBC procedure is applied before
harmonic bond potential is calculated, than the opposite nanotube
atoms should be (already) seen as neighboring. This looks the
Dear GMX users:
Is OPLSAA forcefield data already available for POPC membranes. I am
interested in simulation of proteins in POPC membrane.
Thank you.
Best Regards
Karthi.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the
I found the -multi version of that tutorial a bit temperamental...
Michael Shirts suggested that double precision is more reliable for
expanded ensemble. Hopefully he can chime in in a day or two.
Mark
On Thu, Sep 26, 2013 at 9:00 PM, Christopher Neale
chris.ne...@mail.utoronto.ca wrote:
Dear
Thank you Mark.
I actually found that it crashed wihout the -multi part (no hamiltonian
exchange).
The command that I used was: mdrun -nt 1 -deffnm ethanol.1 -dhdl
ethanol.1.dhdl.xvg
If I use the double precision version, there is no segfault. That's a working
solution, but it is worrysome.
Just to be clear, is this the expanded ensemble version of the calculation?
On Thu, Sep 26, 2013 at 5:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote:
I found the -multi version of that tutorial a bit temperamental...
Michael Shirts suggested that double precision is more reliable for
My mistake I still get a segfault even when using double precision. (EM
doesn't help, nor does switching to Berendsen pressure coupling).
Note that I can stop the segfault when running at init-lambda-state = 0 if I
set:
couple-lambda0 = none
couple-lambda1 = none
No, this is not the expanded ensemble version. It's the initial Running the
calculation with Gromacs section straight out of
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy
I get the segfault with a single run (at any of the 9 individual lambda values).
I thought I had just managed to solve the issue :)
If you look at the soft core parameters, there are two types listed --
one with sc-r-power = 48, and one with sc-r-power = 6. The sc-r-power
are more stable with single precision calculations.
I have changed the files on the website to make the
And with this change, single is running fine as well.
This was a known issue, but was only documented in the expanded.mdp
files, which was an oversight. After this, I switched so the default
is less likely to cause problems. Because of some theory improvements
developed in the group in free
Agreed, the following parameters do not segfault in single or double precision:
sc-alpha = 0.5
sc-power = 1
sc-r-power = 6
Same goes for http://bugzilla.gromacs.org/issues/1306
The following parameters give a segfault in single precision but are ok
Sounds like we've resolved all the confusion. Thanks for prompt help
in making this clearer and better.
On Thu, Sep 26, 2013 at 7:01 PM, Christopher Neale
chris.ne...@mail.utoronto.ca wrote:
Agreed, the following parameters do not segfault in single or double
precision:
sc-alpha
Dear Users:
I'm having difficulty running MBAR after some free energy calculations (MBAR
via alchemical-gromacs.py obtained from alchemistry.org).
The input options to alchemical-gromacs.py have obviously changed since the
site at
Dear Karthi:
As far as I am aware, there is no OPLSAA lipid force field. I have used Berger
lipids with OPLSAA protein
( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing
a UA lipid with an AA protein
so be aware of possible problems arising out of that.
Charmm has
On 9/26/13 10:47 PM, Christopher Neale wrote:
Dear Karthi:
As far as I am aware, there is no OPLSAA lipid force field. I have used Berger
lipids with OPLSAA protein
( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing
a UA lipid with an AA protein
so be aware of
Dear Gigo:
I've never used tip5p, but perhaps you could add some LJ terms to the opls_120
definition,
do your minimization, then remove the fake LJ term on opls_120 and run your MD?
If that doesn't work, then you might be able to minimize your system using
FLEXIBLE tip3p
water and then use a
Thank you Sir!
Regards
Kavya
On Fri, Sep 27, 2013 at 12:52 AM, Tsjerk Wassenaar tsje...@gmail.comwrote:
Hi Kavya,
genconf -nbox 3 3 3
Cheers,
Tsjerk
On Thu, Sep 26, 2013 at 6:24 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
For some analysis I require the 27 periodic
Thanks for the quick reply sir.
So, does it mean I can apply trjcat on the processed xtc files???
On Thu, Sep 26, 2013 at 10:25 PM, Tsjerk Wassenaar tsje...@gmail.comwrote:
Hi Venkat,
These options are 'frame intrinsic' or 'history independent', unlike -pbc
nojump.
Cheers,
Tsjerk
On
Dear Gromacs Specialists,
I am searched force field for Titanium (Ti) element. Parameters consist of
sigma and epsilon. Can you help me, Please?
Best Regards
Sara
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive
Dear Users,
I am running Protein-Ligand MD simulations. Whenever, i get to do the
Position restrain run of both my protein and ligand, i get this error;
Making 1D domain decomposition 4 x 1 x 1
starting mdrun 'Protein in water'
5 steps,100.0 ps.
step 0
Step 8, time 0.016 (ps) LINCS
Thank you all for the reply, now I'm much less confuse and thank you
David for the paper.
I wanted to try implicit simulations because I need to speed up a bit my
simulations...but I think that now I'll try something else (coarse
grained/remd).
cheers
Fra
On Mon, 23 Sep 2013, at 08:28 PM,
OK seems it is my self-post, but incase anyone finds it, so they are not
mislead by the above.
After few more trial and fails, I think currently there is no tool to
assemble a periodic system from residues. So neither the approach with
specbonds, nor the periodic_molecule work for this case.
If it may be of help this paper
(http://www.ncbi.nlm.nih.gov/pubmed/?term=Systematic+Validation+of+Protein+Force+Fields+against+Experimental+Data)
compares several force field with experimental data.
It was useful to me at the time I read it.
cheers
Fra
--
View this message in context:
I found this list useful:
http://md.chem.rug.nl/cgmartini/index.php/blog/265-comparingforcefields
http://md.chem.rug.nl/cgmartini/index.php/blog/269-jungle2
On Wed, Sep 25, 2013 at 4:16 PM, fcarb frac...@myopera.com wrote:
If it may be of help this paper
(
On 9/25/13 4:54 AM, mohammad agha wrote:
Dear Gromacs Specialists,
I am searched force field for Titanium (Ti) element. Parameters consist of
sigma and epsilon. Can you help me, Please?
http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species
I sincerely doubt that a
On 9/25/13 6:05 AM, MUSYOKA THOMMAS wrote:
Dear Users,
I am running Protein-Ligand MD simulations. Whenever, i get to do the
Position restrain run of both my protein and ligand, i get this error;
Making 1D domain decomposition 4 x 1 x 1
starting mdrun 'Protein in water'
5 steps,100.0
Dear Mark
The UNIX tool diff is your friend for comparing files.
Thanks for your suggestion. I used diff and sdiff toll
for comparing 2 files (before and after correction).
diff old.gro new.gro
These tolls did not give me any output file or text
containing difference between 2 files.
In this
Thank you very much from your answer.
Best Regards
Sara
From: Justin Lemkul jalem...@vt.edu
To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Sent: Wednesday, September 25, 2013 3:07 PM
Subject: Re: [gmx-users] force
Hi All,
I have a dopc+50% cholesterol bilayer. I want to selectively choose the
upper and lower leaflets. I used g_select the following way
g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname Cholesterol
and z6' (6 is the COM of my box)
I am getting the following error.
Possible bug:
Dear all,
I would like to calculate how three dihedrals in my
protein are evolving during the simulation time, but I don't understand
which is the correct command to do.
In particular, I would like to
know:
- what is the value of a specified dihedral (in degrees)
- if
this value changes
Hello,
On Wed, Sep 25, 2013 at 5:48 PM, rajat desikan rajatdesi...@gmail.comwrote:
I have a dopc+50% cholesterol bilayer. I want to selectively choose the
upper and lower leaflets. I used g_select the following way
g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname Cholesterol
and
Thank you very much. My bilayers were initially built with packmol which is
probably why z6 worked. I will keep this in mind.
On Wed, Sep 25, 2013 at 9:46 PM, Teemu Murtola teemu.murt...@gmail.comwrote:
Hello,
On Wed, Sep 25, 2013 at 5:48 PM, rajat desikan rajatdesi...@gmail.com
wrote:
I
Basic question: How do I verify that the right atoms were chosen in the
index file? There are a lot of atoms.
On Wed, Sep 25, 2013 at 9:52 PM, rajat desikan rajatdesi...@gmail.comwrote:
Thank you very much. My bilayers were initially built with packmol which
is probably why z6 worked. I will
On 9/25/13 12:24 PM, rajat desikan wrote:
Basic question: How do I verify that the right atoms were chosen in the
index file? There are a lot of atoms.
Pass the index file to trjconv and use it to parse out the atoms in the group
from the original coordinate file.
-Justin
On Wed, Sep
On 9/25/13 12:08 PM, Anna MARABOTTI wrote:
Dear all,
I would like to calculate how three dihedrals in my
protein are evolving during the simulation time, but I don't understand
which is the correct command to do.
In particular, I would like to
know:
- what is the value of a specified
If diff says there are no changes, then you're not comparing with the file
you changed...
On Sep 25, 2013 1:59 PM, shahab shariati shahab.shari...@gmail.com
wrote:
Dear Mark
The UNIX tool diff is your friend for comparing files.
Thanks for your suggestion. I used diff and sdiff toll
for
Dear prof.
The format of parameters is convenient to the software of Amber and not
to gromacs. if i use the parameters i must use some tools to convert it to the
itp format for gromacs. so i use acpype to get itp format.
i just doubt that i use amber99sb for protein and AM1-BBC for
Dear list members,
I am trying to simulate an infinite layer of quartz in Gromacs. Due to my
needs (afterwards I need to place a large molecule on top of it) the surface
must be at least 12x12 nm^2. I generated the input files from a pdb file of
the structure, and adapted the OPLS force field to
Dear all,
I have sent this e-mail to the gmx-users mailing list for a few days, but without any reply until now. I'm not sure if it has something to do with the format, because the link cant be opened when I search the mailing list. So this time I use the plain text and send it once more, would
Dear all,
I have sent this e-mail to the gmx-users mailing list for a few days, but
without any reply until now. I'm not sure if it has something to do with the
format, because the link can’t be opened when I search the mailing list. So
this time I use the plain text and send it once more,
Dear Justin
I'm simulating gold nanoparticle interaction with protein by OPLSAA forcefield.
I'm confused for selection an ensemble for my md run. I did energy minimization
by NPT . then I did the MD by NVT. I did it because of studying of two paper
that were similar to my project
Hello,
On Tue, Sep 24, 2013 at 8:39 AM, Venkat Reddy venkat...@gmail.com wrote:
I have been using the new tool gmx gangle. My actual intention is to
calculate the orientation between any two same molecules (say cholesterol)
throughout the trajectory and there are 40 cholesterol molecules. But
Dear GMXers,
Since I am interested in interactions of lone electron pairs of water
oxygen within the active site of an enzyme that I work on, I decided to
give TIP5P a shot. I use OPLSAA. I run into troubles very fast trying to
minimize freshly solvated system. I found on the gmx-users
You should be able to minimize with CG and TIP5P by eliminating
constraints, by making the water use a flexible molecule, e.g. define
= -DFLEXIBLE (or something). Check your water .itp file for how to do
it.
Mark
On Tue, Sep 24, 2013 at 10:25 PM, gigo g...@ibb.waw.pl wrote:
Dear GMXers,
Since
Dear all,
I have been trying to evaluate a paper that used amber99 with SPC water to
simulate a protein. How would this affect the results, is it important? I
googled for a bit, all I found was:
Amber, charmm and OPLS-AA were developed with TIP3P, and that should be
the default. Except that
The FF+water combinations still work the same way they did 3 years
ago! :-) The important question is whether validation for the
observables has occurred. (And no relevant problems were seen). If the
paper does not support its decision to mix and match, go and ask them
why it was reasonable!
Mark
Ok, thanks, I may just do that
On Tue, Sep 24, 2013 at 2:42 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
The FF+water combinations still work the same way they did 3 years
ago! :-) The important question is whether validation for the
observables has occurred. (And no relevant problems
On 9/23/13 11:43 PM, Santhosh Kumar Nagarajan wrote:
Justin..
I understand the problem..
But.. How to generate a .rtp file myself..
Study existing examples, read manual section 5.6.1, and fire up a text editor.
-Justin
--
==
Justin A.
On 9/24/13 7:16 AM, aixintiankong wrote:
Dear prof.
The format of parameters is convenient to the software of Amber and
not to gromacs. if i use the parameters i must use some tools to convert it to
the itp format for gromacs. so i use acpype to get itp format.
i just doubt
On 9/24/13 2:40 PM, fatemeh ramezani wrote:
Dear Justin
I'm simulating gold nanoparticle interaction with protein by OPLSAA
forcefield. I'm confused for selection an ensemble for my md run. I did
energy minimization by NPT . then I did the MD by NVT. I did it because of
Let's take a step
Dear Mark,
Thank you for your reply. Unfortunately, TIP5P is completely rigid and
the FLEXIBLE define will not change it. Any other ideas?
Best,
g
On 2013-09-24 23:51, Mark Abraham wrote:
You should be able to minimize with CG and TIP5P by eliminating
constraints, by making the water use a
Hi every body
in order to protein- ligand docking, energy minimization was done by
GROMACS. I did the following steps for insulin pdb file:
1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce
2- grompp -f em.mdp -c test.pdb -p topol.top -o em.tpr
3-mdrun -v -deffnm em
4- editconf -f
I tried minimizing a box of cyclohexanes and water. The first frame is
fine, but after that seemingly random lines form in vmd with the
cyclohexanes. The waters seem to minimizing just fine though.
I am sure I am just doing something extremely silly and I just don't know
it because of ignorance.
That said, there is an spc.itp within the AMBER subdirectories that needs
to be
#included more explicitly, i.e. #include amber99sb.ff/spc.itp
May I ask why you are using SPC? The AMBER force fields were parametrized
with
TIP3P, so I see no viable reason to use a different water model.
Ah, fixed
Dear Gromacs users,
I’m trying to calculate the binding enthalpy of a host molecule with a
guest molecule in vacuum. I cannot perform QM calculations because some
systems I’m studying are too large.
I know that free energy calculations are possible with Gromacs, but they
require some
Hello all,
It is not a gromacs problem per se, but I hope that some gromacs users can
help me. I would to do simulations of phospholipid bilayers with the TIP4P/2005
water model. I have downloaded in the Klauda's website several bilayer starting
conformations. However, since CHARMM uses the
Dear John -
I think you can achieve the goal even faster if you just define two
groups, such as MOL1 and MOL2 in MDP and then see the interaction
energy between them using g_energy.
5% is a decent agreement. Usually, even basis set superposition error
is larger (if you include this correction).
Dear Jonathan -
Is it not a PBC effect? Try to display atoms as spheres - it will look
better. Otherwise, use the options in trjconv to remove PBC in the
visualized structure(s).
Dr. Vitaly V. Chaban
On Mon, Sep 23, 2013 at 9:22 AM, Jonathan Saboury jsab...@gmail.com wrote:
I tried minimizing
I am confused. Why do you want 4-sites water?
Dr. Vitaly V. Chaban
On Mon, Sep 23, 2013 at 10:36 AM, ABEL Stephane 175950
stephane.a...@cea.fr wrote:
Hello all,
It is not a gromacs problem per se, but I hope that some gromacs users can
help me. I would to do simulations of phospholipid
Hello,
Because I want to compare the simulation results (essentially water dynamic)
with previous simulations of reverse micelles, micelles carried out with the
same water model.
Stephane
--
Message: 8
Date: Mon, 23 Sep 2013 10:45:56 +0200
From: Dr. Vitaly
Using trjconv -f traj.xtc -o confout.gro -dump 1500, I routinely
get the following error:
Select a group: 0
Selected 0: 'System'
Reading frame 0 time0.000
Precision of traj.xtc is 0.004 (nm)
Using output precision of 0.001 (nm)
Back Off! I just backed up confout.gro to
On 9/23/13 3:08 AM, marzieh dehghan wrote:
Hi every body
in order to protein- ligand docking, energy minimization was done by
GROMACS. I did the following steps for insulin pdb file:
1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce
2- grompp -f em.mdp -c test.pdb -p topol.top
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