Thanks again
That is it what I was asking. I have seen the topology files of t4-lysozyme
with its ligand. It was provided by alchemistry.org tutorial. Can I change
the topology accordingly.
Another thing is the charge on the ligand molecule. How this will be
handled in free energy calculations.
W
well
if you are confident of your simulation you may definitly go ahead with
this ff
otherwise you will have to change the ff for simulation too
i think this is not rational to simulate the system with one ff and then
change the ff for free energy calculations
good luck
On Jan 7, 2017 2:01 PM, "t
Thanks Amir Zeb for your reply
I have read in literature about the FEPsetup to parametrize the complex
file (protein+drug) for simulation. This setup builds files based on amber.
Since I have previously used 54a7ff to simulate the protein and drug and
topology files were generated from ATB in gromo
alright
why do you care of forcefield in terms of free energy calculations?
do you have literature in reference for your protein simulated with a
specific ff?
On Jan 7, 2017 1:38 PM, "tasneem kausar" wrote:
> mm/pbsa calculates binding energy. I have used that.
>
> On Sat, Jan 7, 2017 at 10:00 A
mm/pbsa calculates binding energy. I have used that.
On Sat, Jan 7, 2017 at 10:00 AM, Amir Zeb wrote:
> hello
> you may use mm/pbsa compiled with gromacs to calculate free energy
> all the best
>
> On Jan 7, 2017 1:27 PM, "tasneem kausar"
> wrote:
>
> > Dear gromacs users
> >
> > It is first ti
hello
you may use mm/pbsa compiled with gromacs to calculate free energy
all the best
On Jan 7, 2017 1:27 PM, "tasneem kausar" wrote:
> Dear gromacs users
>
> It is first time I am trying to perform free energy calculation of protein
> and drug complex. I am following Justin' s tutorial of mehta
Dear gromacs users
It is first time I am trying to perform free energy calculation of protein
and drug complex. I am following Justin' s tutorial of mehtane in water.
That calculation are performed on a neutral system. If the ligand molecule
has charge what are the provisions that could be taken i
Hi Szilárd,
Thanks for responding. Yes, those systems are indeed expensive, and our
main objective here wasn't really bang for the buck. What we want is the
fastest possible single node for the money, and if that means an extra
$5-10K, we're okay with that. The machine we want to build isn't
Hi,
You find find this paper relevant (
https://www.ncbi.nlm.nih.gov/pubmed/22034434).
Ruan
On Fri, Jan 6, 2017 at 5:14 PM, Academic Research
wrote:
> Hello everyone,
>
>
> I have computationally designed several synthetic proteins that are not
> found in nature.
>
>
> My lab has limited resou
Hello everyone,
I have computationally designed several synthetic proteins that are not found
in nature.
My lab has limited resources for wet lab work and so I would like to use
gromacs to simulate these proteins in water and see weather they unfold or
aggregate. I know the best way is to a
On 1/6/17 2:41 PM, liming_52 wrote:
Thank you for reppy. The full information is as follows:
$ gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce
:-) GROMACS - gmx pdb2gmx, VERSION 5.1.4 (-:
GROMACS is written by:
Emile Apol Ros
Thank you for reppy. The full information is as follows:
$ gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce
:-) GROMACS - gmx pdb2gmx, VERSION 5.1.4 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen
Hi Mark,
Thanks.
Things work fine with Gromacs 2016.
Thanks,
Sxn
On Dec 12, 2016 4:49 PM, "Mark Abraham" wrote:
> Hi,
>
> We periodically hear reports of people unable to checkpoint reliably with
> some forms of replica exchange, but no clear pattern has emerged, and
> nobody has yet shared a
On 1/6/17 2:22 PM, faride badalkhani wrote:
Dear GROMACS users,
I have performed pulling simulations on polymer-drug complex an each window
was obtained by an increment of 1 Å from the previous window, and for each
window, 5 ns MD simulation was performed. But the histogram for the first 6
win
Hi there,
Farideh Khamseh (farideh.kham...@gmail.com) invited you to view the file "
histo.xlsx " on Dropbox.
View file[1]
Enjoy!
The Dropbox team
[1]: https://www.dropbox.com/l/scl/AAAtNLZS5tTOC0kssvnl8e0ms-GkfMQbWEw
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http://www.g
On 1/6/17 1:58 PM, liming_52 wrote:
Dear Gromacs users,
I am trying to run a md using 4n6p.cif, which was obtained from PDB. I
converted the file into pdb format using DS4.1, and got the file named
lactoferrin.pdb. When I directly run
the command "gmx pdb2gmx -f lactoferrin.pdb -o lactoferri
Dear GROMACS users,
I have performed pulling simulations on polymer-drug complex an each window
was obtained by an increment of 1 Å from the previous window, and for each
window, 5 ns MD simulation was performed. But the histogram for the first 6
windows is as follows:
https://www.dropbox.com/s/2
Hi there,
Farideh Khamseh (farideh.kham...@gmail.com) invited you to view the file "
histo.xlsx " on Dropbox.
View file[1]
Enjoy!
The Dropbox team
[1]: https://www.dropbox.com/l/scl/AABx-njEs4l7Xh-vbDVRhAm9tmezAB5fXO0
--
Gromacs Users mailing list
* Please search the archive at
http://www.g
Dear Gromacs users,
I am trying to run a md using 4n6p.cif, which was obtained from PDB. I
converted the file into pdb format using DS4.1, and got the file named
lactoferrin.pdb. When I directly run
the command "gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water spce",
the program runs an
On 1/6/17 1:34 PM, ABEL Stephane 175950 wrote:
ello,
A quick question :
It is possible to save the velocities (in a trr file) for only selected atoms
"during" a simulation as we can do in case of the xtc files by using a the mdp
option compressed-x-grps?
No.
If storage is an issue, run
On 1/6/17 2:24 AM, Dilip H N wrote:
no...
I want to create 300 molecules of ammonia...
Well, you asked about BF3, so you got an answer about BF3 :)
how can i create 300 molecules of ammonia and then get it in .pdb file
format..??
For a simple molecule like NH3 you can easily write the
On 1/5/17 3:40 AM, Aditya Padhi wrote:
Dear Gromacs users,
I am trying to evaluate entropic contributions for a protein-protein
complex using the gmx covar module and then gmx anaeig. When I directly run
the command "gmx covar -f prod.xtc -s prod.tpr -n index.ndx -o eigenval.xvg
-v eigenval.tr
On 1/5/17 3:58 PM, 大木啓輔 wrote:
Dear Gromacs users
I want to calculate Potential Energy of segment of the structure.
For example, segment that coordinations in z axis are 7.2 Å in the structure.
I could specify that segment of atom numbers by writing index file.
But gmx energy has no option o
On 1/6/17 1:58 AM, Nivedita Rai wrote:
Dear gromacs User,
I am running *protein ligand complex* simulation by
following the Beven lab tutorial. while production run im getting two notes
such as:
NOTE 1 [file topol.top]:
The largest charge group contains 11 atoms.
Since
ello,
A quick question :
It is possible to save the velocities (in a trr file) for only selected atoms
"during" a simulation as we can do in case of the xtc files by using a the mdp
option compressed-x-grps?
Thanks
S
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http:/
Dear Gromacs users,
I've been attempting simulated tempering (ST) in Gromacs to study gel-phase
bilayers (~15000 atoms), but I've been encountering some difficulties. I've
been following similar steps in the expanded ensemble tutorial on
alchemistry.org and adapting them for ST. The system I am st
Dear Gromacs users,
I am comparing the PMF simulations using the Gromacs 2016 version with old
version 5.0.5. I found the *gmx wham* in Gromacs 5.0.5 couldn't process the
tpr files generated by Gromacs 2016.1 . (tpx version 100 vs. tpx version
110). The new Gromacs 2016.1 can process the tpr files
Dear Hannes,
Yes, I mean David Mobley's tool.
I checked it out, however it crashed exactly in the *.xvg file (prd.15.xvg
and afterward) in which additional \lambada getting involved. I invoked
below command to get rid of other method except TI:
"alchemical_analysis -p prd. -u kcal -f 20 -o 100dis
Dear gmx users,
We are considering buying a GPU workstation in which most of calculations will
be run using gromacs.
I have searched the mailing list for a comparison of gromacs 5 and gromacs 2016
performance on multiple GPU runs. For gromacs 5, I found this one
http://onlinelibrary.wiley.com
Hi Alex,
Benchmarks of quad-socket Intel machines are rare because AFAIK such
systems are mighty expensive and you will not get good bang for buck with
them, especially if you combine these pricey nodes/CPUs with the old and
slow K80s.
The only reason to get E7 is if >=4 sockets or >1.5 TB memory
On Fri, Jan 6, 2017 at 8:21 AM, Subashini .K wrote:
> Hi Gromacs users,
>
>
> I am new to Gromacs. Have installed it in windows 7.
>
> Had followed the instructions this website
> https://winmostar.com/en/gmx4wm_en_win.html
>
>
> How to run a test file through cygwin? Can someone help?
What do y
Dear Raag,
Where would those extra ions go? If you need a higher number density of ions
than the solvent (assuming the box is full of water, plus the protein) you will
most likely raise the pressure of the system to bizarre levels. What ion
concentration are you aiming for? Is that a reasonable
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