Dear Ishrat,
I recommend this article and references therein for TMAO + urea parameters:
http://dx.doi.org/10.1021/jacs.7b11695.
Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Bi
Hi,
The urea model of Lorna Smith (
https://pubs.acs.org/doi/abs/10.1021/jp030534x
) should be compatible with GROMOS force field.
Best regards
Alessandra
On Wed, Mar 4, 2020 at 7:00 AM ISHRAT JAHAN wrote:
> Dear all,
> I want to do MD simulation of protein in urea and urea-TMAO mixture. Can
>
Dear all,
I want to do MD simulation of protein in urea and urea-TMAO mixture. Can
you suggest me which force field would be better for urea and urea tmao
mixture? Is Kast-2016 TMAO model is compatible with gromos54a5 force field
as I have done the simulation of protein with this force field. Any
s
Dear all,
I want to do MD simulation of protein in urea and urea-TMAO mixture. Can
you suggest me which force field would be better for urea and urea tmao
mixture? Is Kast-2016 TMAO model is compatible with gromos54a5 force field
as I have done the simulation of protein with this force field. Any
s
Dear Gmx Experts,
I would like to simulate hydroxyapatite with short peptides. I would like
to use my own prepared surface which consists of a surface and a hole. I
looked for some possible parameters. INTERFACE force field is compatible
with GROMACS, which contains a number of small surfaces and
Hi,
You can use acpype to build the amber forcefield parameters. Each force
field have corresponding servers which can make .tpr file for you. You can
easily run simulation with that file.
On Mon 10 Jun, 2019, 6:43 PM antonia vyrkou, wrote:
> Dear all,
>
> I want to simulate an organometalli
Dear all,
I want to simulate an organometallic compound and how it affects an
enzyme's function using Gromacs but I am having trouble finding suitable
force field parameters. If would really appreciate any suggestions for a
Gromacs compatible , Amber compatible force field
Thank you
Antonia
--
On 3/4/19 8:59 AM, Smith, Micholas D. wrote:
Hi Swapnil Bhujbal,
The parameters exist; however, the residue rtp file may not have entries for
the phosphorylated residues. If you want to use pdb2gmx to you will need to add
these residues into the rtp file associated with the force-field.
Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Swapnil
Bhujbal
Sent: Monday, March 4, 2019 8:12:37 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Force field
Dear Users,
I'm performing ligand-protein simulation. My protein has phosphothreonine
and phosphoserine residues. So I have cheched this forum and accordingly I
have downloaded Charm36 force field November 2018 (
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs) and kept in my
installation d
hey are space delimited.
Regards,
Peter
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On Behalf Of Matthew
Stoodley
Sent: Thursday, February 21, 2019 12:59 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Force field parameters not known
Hi,
I am currently trying to perform a simulation on a chemical molecular machine
but whenever I try and do the pdb2gmx command and select a force field it comes
up with the message 'the residue DVHY is not recognised'. From my understanding
what I should do is to update the residue in the speci
I am new to gromacs.
I am generating Polymers structures of varying chain length via Avogrado
software. I am not sure about how to generate the .itp file. for a specific
force field, in my case say OPLSAA.
Also in case my polymer is a poly electrolyte how do I assign charges or
how do I let the sy
users-boun...@maillist.sys.kth.se] On Behalf Of Alex
Sent: Sunday, September 30, 2018 12:44 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] force field not found
Yeah, if it is missing bonded parameters, you can always try to find
something similar, at least with OPLS-AA -- don't really know abo
12:44 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] force field not found
Yeah, if it is missing bonded parameters, you can always try to find
something similar, at least with OPLS-AA -- don't really know about the
other ff.
Alex
On 9/29/2018 8:58 PM, paul buscemi wrote:
>
Yeah, if it is missing bonded parameters, you can always try to find
something similar, at least with OPLS-AA -- don't really know about the
other ff.
Alex
On 9/29/2018 8:58 PM, paul buscemi wrote:
Alex,
I wanted to practice some more with x2top using a simple CH3 -( CH2)14 -Ch3
pdb mode
Alex,
I wanted to practice some more with x2top using a simple CH3 -( CH2)14 -Ch3
pdb model. oplsaa works fine, but not 54a7 FF generating the erro “ cannot
find forcefield for C “ Th two CH3’s do not cause the error found but the
fourteen CH2’s.
In the ffbonded.itp bond angle types i see
I have already mailed them... waiting for their reply..
On Sat, 7 Jul 2018, 11:22 pm Mark Abraham, wrote:
> Hi,
>
> Your other good approach is to contact the authors to ask them to share
> their methodology fully, ie force field files.
>
> Mark
>
> On Sat, Jul 7, 2018, 13:47 Soham Sarkar wrote
Hi,
Your other good approach is to contact the authors to ask them to share
their methodology fully, ie force field files.
Mark
On Sat, Jul 7, 2018, 13:47 Soham Sarkar wrote:
> Dear All,
> Can anyone please tell me, where from I get the parameters for
> Osmotic, Kast, Netz force f
Dear All,
Can anyone please tell me, where from I get the parameters for
Osmotic, Kast, Netz force field like the files OPLS, CHARMM which is
already in GROMACS? I have got the files for the KBFF force field but not
these three. The paper by Dias and group
https://journals.aps.org/prl
On 6/19/18 4:35 PM, Wahl, David M wrote:
Hello,
I am working on a molecular dynamics simulation in GROMACS and am curious as to
which force field will be the best to run a simulation on a small organic
molecule containing carbon, nitrogen, oxygen and hydrogen. Through some
research it se
I think you should recalculate charged of atoms of that molecule, the other
properties can used from GAFF
URL: https://qvu.netlify.com/#/
On Wed, Jun 20, 2018 at 3:36 AM Wahl, David M wrote:
> Hello,
>
>
> I am working on a molecular dynamics simulation in GROMACS and am curious
> as to which f
I think you should recalculate charged of atoms of that molecule, the
other properties can used from GAFF
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Hello,
I am working on a molecular dynamics simulation in GROMACS and am curious as to
which force field will be the best to run a simulation on a small organic
molecule containing carbon, nitrogen, oxygen and hydrogen. Through some
research it seems that the general Amber force field (gaff)
Hi,
i am trying to parametrize a Metal-Organic-Framework for later gromacs
simulations. Does anybody have experience in deriving parameters like
force constants completely from theory? I know that there are techniques
doing it with DFT-calculations but i would like to know other methods as
we
On 4/13/18 6:26 AM, rose rahmani wrote:
Hello,
I use AMBER force field.
So, how about periodic structures? like inorganic nanosheet and nanotubes?
One would never attempt to do parametrization directly on a full,
periodic structure, largely because (1) it's not possible/practical and
(2) y
Hello,
I use AMBER force field.
So, how about periodic structures? like inorganic nanosheet and nanotubes?
Thank you so much
On Fri, 13 Apr 2018, 14:50 Paul bauer, wrote:
> Hello,
>
> this depends on the force field you are using. Some of them use
> parameters from a QM optimization and partia
Hello,
this depends on the force field you are using. Some of them use
parameters from a QM optimization and partial charge calculation.
But even then you need to be careful that the results from the QM are
not just random numbers :)
But I'm not sure myself how I would tackle something like M
On Fri, 13 Apr 2018, 14:35 Paul bauer, wrote:
> Hello,
>
> I would recommend that you check relevant publications for the
> simulation of magnetite if people have tried to simulate it in solvent.
> I could not find anything during a short search, but maybe you'll be
> more successful. :)
> If the
Hello,
I would recommend that you check relevant publications for the
simulation of magnetite if people have tried to simulate it in solvent.
I could not find anything during a short search, but maybe you'll be
more successful. :)
If there are no published parameters in the literature you will
Dear gromacs users,
I want to simulate a protein in different concentration of Fe3O4.
How to obtain force field parameters of Fe3O4?
Any help will highly be appreciated.
Best,
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Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_
On 1/15/18 1:27 PM, Harsha Ravishankar wrote:
Hello Justin,
Thanks for the reply. I only make use of Charmm GUI to generate the
membrane patch, as I need to orient my protein in a particular orientation.
However when I made use of the .itp forcefield files in gmx grompp -f
ions.mdp -c solvate.
Hello Justin,
Thanks for the reply. I only make use of Charmm GUI to generate the
membrane patch, as I need to orient my protein in a particular orientation.
However when I made use of the .itp forcefield files in gmx grompp -f
ions.mdp -c solvate.gro -p topol.top -o ions.tpr I get errors stating
On 1/15/18 9:45 AM, Harsha Ravishankar wrote:
Dear All,
I am a beginner with Gromacs and simulations and I want to simulate a
membrane and protein complex with the membrane comprising of 5 different
lipid molecules. The membrane was generated with Charmm-GUI and the
appropriate Gromacs paramet
Dear All,
I am a beginner with Gromacs and simulations and I want to simulate a
membrane and protein complex with the membrane comprising of 5 different
lipid molecules. The membrane was generated with Charmm-GUI and the
appropriate Gromacs parameters for the different lipids were also obtained.
Hi,
There's lots of discussion in the reference manual, and also in the force
field files themselves.
Mark
On Mon, Jan 8, 2018 at 4:28 PM Lara rajam wrote:
> Dear GMX users
> I would like to know where we would get the force field information in GMX
> .
> Like in NAMD the Topology and parm fil
>I would like to know where we would get the force field information in GMX
The answer is obvious: read manual (chapter 4 I"nteraction function and force
fields" and 4.10 "Force field"). The FF files are situated in
/usr/share/gromacs/top (for my PC) and are transparent enouth.
--
Gromacs Us
Dear GMX users
I would like to know where we would get the force field information in GMX
.
Like in NAMD the Topology and parm file tells the details of the atom
labeling,charge,connectivity etc., Simillarly where I could see the Gromos
force field insights.
Please provide me links or tutorials tha
Hi,
Thanks for the tip, I brought the website back up. Most of the relevant
force fields are in the repo, however.
Mark
On Mon, Dec 4, 2017 at 7:54 PM Zahedeh Bashardanesh
wrote:
> Hi,
>
> Does anybody know where else to get the reliable amber force field package
> for gromacs except from grom
Hi,
Does anybody know where else to get the reliable amber force field package
for gromacs except from gromacs website? The webpage has been down since
Saturday.
Best,
---
Zahedeh Bashardanesh, Ph.D. Candidate
Dep
Hi Justin,
just for testing, I applied cgenff_charmm2gmx.py with
charmm36-nov2016.ff as it has the same CGenFF version:
--Version of CGenFF detected in
/usr/local/gromacs/share/gromacs/top/charmm36-nov2016.ff/forcefield.doc
: 3.0.1
But I still get the same warnings and errors.
Would you s
On 11/3/17 10:33 AM, Hermann, Johannes wrote:
Hey Justin,
thanks - again - for your reply!
Now I get duplicated parameters warnings and errors:
WARNING 1 [file fmn.prm, line 5]:
Overriding Bond parameters.
old: 0.1295 405848 0.1295
405848
n
Hey Justin,
thanks - again - for your reply!
Now I get duplicated parameters warnings and errors:
WARNING 1 [file fmn.prm, line 5]:
Overriding Bond parameters.
old: 0.1295 405848 0.1295
405848
new: CG2R64 NG2D1 1 0.1414 255224.0
On 11/3/17 8:17 AM, Hermann, Johannes wrote:
Dear Justin,
thanks for the hint with the CHARMM-formatted topology and parameter
files! That is great help! I had a different atom number compared to
NAI and NADH because I had a different (non-physical) protonation
state. The text drawing help
Dear Justin,
thanks for the hint with the CHARMM-formatted topology and parameter
files! That is great help! I had a different atom number compared to NAI
and NADH because I had a different (non-physical) protonation state. The
text drawing helped me a lot to figure out the few Nomenclature
d
On 11/2/17 12:05 PM, Hermann, Johannes wrote:
Dear Justin, dear all,
thank you for your reply. I will test the web server when I have
managed to generate the mol2 file for FMN.
I had a look in the rtp file of charmm36 ff and I detected that there
are three "NADHs": NAD1 , NAI, and NAD1. N
Dear Justin, dear all,
thank you for your reply. I will test the web server when I have managed
to generate the mol2 file for FMN.
I had a look in the rtp file of charmm36 ff and I detected that there
are three "NADHs": NAD1 , NAI, and NAD1. NAI is the pdb 3 letter code
for the reduced form
As far as I see others just replace selenium with sulphur, convert of
selenomethionine to methionine
like:https://bmccancer.biomedcentral.com/articles/10.1186/1471-2407-14-775
On Wednesday, November 1, 2017, 8:24:10 AM GMT+2, Seera Suryanarayana
wrote:
Dear gromacs users,
I have
Dear gromacs users,
I have to do simulations for a peptide which has the selinomethionine. But
regular force fields from gromacs has no information for this residue.
kindly give me information if is there any force field for
selinometheoinine.
Thanks in advance
Surya
Graduate student
India.
--
G
On 10/30/17 10:58 AM, Hermann, Johannes wrote:
Dear all,
I want to simulate a complex consisting of a protein, FMN, and NADH. I
have two problems/questions:
1) In the "CHARMM36 all-atom force field (March 2017)" parameters for
NADH are present. But apparently I am using a wrong atom naming
Dear all,
I want to simulate a complex consisting of a protein, FMN, and NADH. I
have two problems/questions:
1) In the "CHARMM36 all-atom force field (March 2017)" parameters for
NADH are present. But apparently I am using a wrong atom naming
convention (I copied / pasted NADH from a pdb en
Hi!
I acetylated K40 my heterodimer's PDB file using PyTMs in PyMOL. Now I need
to simulate it using GROMACS. Which force field would be the best for this
purpose?
Thank you in advance!
Regards,
Raag
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* Please search the archive at
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On 2/6/17 9:08 AM, Amir Zeb wrote:
Hello gmx users,
I'm wondering which would be the best force field to create topology for
cobalt. I tried different ff but none of them get the task. I searched the
mailing archive too but I couldn't get the way to solve the issue.
Dr. Justin has just mention
Hello gmx users,
I'm wondering which would be the best force field to create topology for
cobalt. I tried different ff but none of them get the task. I searched the
mailing archive too but I couldn't get the way to solve the issue.
Dr. Justin has just mentioned (https://www.mail-archive.com/gmx
us
Thank you very much Alex :)
On Thursday, December 22, 2016, Alex wrote:
> Sorry to hear this. There is a good chance your reviewer is being an
> obtuse donkey. As a fellow modeler and also a referee, I'd be much more
> worried if someone _did not_ use a standard and well-tested description for
>
Sorry to hear this. There is a good chance your reviewer is being an
obtuse donkey. As a fellow modeler and also a referee, I'd be much more
worried if someone _did not_ use a standard and well-tested description
for ions.
Best of luck! :)
Alex
On 12/21/2016 11:40 PM, Maryam Kowsar wrote:
Thank you Alex. Actually I used Amber since I havent found any better force
fields for nonbonded interactions in my system. It worked fine, but that
was questioned by a reviewer of my submitted paper, though I provided
references.
On Wednesday, December 21, 2016, Alex wrote:
> Hi Maryam,
>
> I a
Hi Maryam,
I am not really sure what "most proper" means when it comes to MD
simulations, but I think if we're talking about vdw/electrostatics, AMBER
and OPLS-AA are very close and have been used widely in the presence of
things like CNTs and graphene... If there's any particular effect you are
u
Dear all
What is the best and most proper force field for ions (like Na+ and Ca2+)
and carbon structured systems interactions? I found a few papers which used
Amber force field. Has anyone worked with or seen any papers in this
regard?
Thanks.
--
Gromacs Users mailing list
* Please search the ar
Thank you very much! How can I transform the gaff (general amber) force field
files into Gromacs force field files? Do you have these tools? I want to
transform *.lib generated by tleap to *.itp and *.top.
--
With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijin
Thank you! I will definitely have a close look at that.
Best regards,
Dawid
2016-12-19 2:33 GMT+01:00 Justin Lemkul :
>
>
> On 12/18/16 12:22 PM, Dawid das wrote:
>
>> Dear All,
>>
>> Have you ever seen a script/tool that allows for transformation of the
>> Gromacs force field files
>> into CHAR
On 12/18/16 12:22 PM, Dawid das wrote:
Dear All,
Have you ever seen a script/tool that allows for transformation of the
Gromacs force field files
into CHARMM force field files? I can see that there is a Pythons script
that does the other
way around.
Also I could use a tool that creates *.psf
Dear All,
Have you ever seen a script/tool that allows for transformation of the
Gromacs force field files
into CHARMM force field files? I can see that there is a Pythons script
that does the other
way around.
Also I could use a tool that creates *.psf file from *.top file. I googled
for that an
Hi,
What atoms do you have in that residue, what's in the c.tdb and .rtp for
GLN in force field and what did you choose for termini?
Mark
On Fri, Dec 9, 2016 at 4:05 PM Seera Suryanarayana
wrote:
> Dear gromacs users,
>
> I have one protein with phosphoserine and phosphothreonine. I want to
>
Dear gromacs users,
I have one protein with phosphoserine and phosphothreonine. I want to
do simulation, but I do not know which force field I have to use. None
of the force field from gromacs has the information of phospho
residues. Then I tried with charm36, but did work. Kindly suggest me
Hi,
I want to model a linear compound that has a ketal component.
While building the OPLSAA topology (.itp) file for this molecule I ran into
not having the C-C-C angle parameterized in -O-(CH3)2C-O-. I have spent
some time looking for a different force field that may have this entire
molecule, w
Hi,
On Fri, May 27, 2016 at 12:55 PM Alexander Alexander <
alexanderwie...@gmail.com> wrote:
> Thanks for your response.
>
> What does "being compatible" mean here, please?
>
That someone has done a bunch of work and presented results that show that
sets of parameters reproduce physically meanin
Thanks for your response.
What does "being compatible" mean here, please?
Actually, the FF of the surface (meanly \sigma and \epsilon in L-J) was
harvested via a series of parametrization of some parameters with the
quantum calculation of the same parameters. So, how can I find the most
compatibl
On 5/25/16 11:05 AM, Alexander Alexander wrote:
Dear Gromacs user,
I am going to simulate the binding free energy of some amino acid to a
metal surface in aqueous solution and also peptide adsorption behavior into
this surface.
I know the force field of the surface as well as the better type
Dear Gromacs user,
I am going to simulate the binding free energy of some amino acid to a
metal surface in aqueous solution and also peptide adsorption behavior into
this surface.
I know the force field of the surface as well as the better type of water
for such a work, but I do not know which ty
My group works with the bicarbonate and similar anions in the context
of CO2 chemisorption.
You must exercise serious caution to assign correct electrostatic
potential at the surface of the anion and account for
hydration/solvation effects within the force field derivation
procedure.
On Fri, S
2015 14:11
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Force field selection for free Bicarbonate molecules
in solution
On 9/4/15 9:07 AM, Faulkner, Matthew wrote:
> Thank you Justin,
>
> Do you know a suitable force field to use for a topolgy from PRODRG? I am
> aware that the t
On 9/4/15 9:07 AM, Faulkner, Matthew wrote:
Thank you Justin,
Do you know a suitable force field to use for a topolgy from PRODRG? I am aware
that the topology from PRODRG may now be of the best quality but I want to run
a short MDS as proof of concept first to see if the events I am interes
.
Regards,
Matthew.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul
[jalem...@vt.edu]
Sent: 04 September 2015 13:58
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Force
On 9/4/15 7:42 AM, Faulkner, Matthew wrote:
I am trying to find a suitable force field for using Bicarbonate in an
aqueous environment in my MDS. I can't find anything where Bicarbonate has
been used this way in gromacs in the literature, does anybody know of a
reference for me or have advice o
:26
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Force field selection for free Bicarbonate molecules
insolution
Matthew,
Quick question, what are you trying to examine with the addition of bicarbonate?
-Micholas
===
Micholas Dean Smith, PhD.
Post-doctoral Research
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Faulkner,
Matthew
Sent: Friday, September 04, 2015 7:42 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Force field selection for free Bicarbonate molecules in
solution
I am trying to find
I am trying to find a suitable force field for using Bicarbonate in an aqueous
environment in my MDS. I can't find anything where Bicarbonate has been used
this way in gromacs in the literature, does anybody know of a reference for me
or have advice on which force filed would be best?
I have ru
The only thing you need is to transfer partial charges. This can be
done using a copy-paste tool.
The Amber FF is within gromacs distribution, so the needed bond
lengths will be picked up implicitly after you specify bonded atoms,
e.g. using x2top or by hand.
On Sat, Aug 22, 2015 at 8:28 AM, N
Hi all,
I am trying to parameterise a new compound in Gromacs (theoretical
compound - my experimental collaborators are still trying to purify and
mass spec it) using the Amber 99sb force field. After asking about, I now
know that in Amber I would take my QM structure run antechamber (or R.E.D
too
thank you all for answering my question
On Monday, August 10, 2015 2:29 AM, Justin Lemkul wrote:
On 8/9/15 5:51 PM, mohammad r wrote:
> Thank you very much Maryam and Justin.unfortunately I am new to gromacs and
> MD.I think that I can acetylate or ammoniate my peptide with -ter at
On 8/9/15 5:51 PM, mohammad r wrote:
Thank you very much Maryam and Justin.unfortunately I am new to gromacs and
MD.I think that I can acetylate or ammoniate my peptide with -ter attachment
to pdb2gmx command. I think it works.What is the different between NH2+ and
NH3 for ammoniation (the grom
Thank you very much Maryam and Justin.unfortunately I am new to gromacs and
MD.I think that I can acetylate or ammoniate my peptide with -ter attachment to
pdb2gmx command. I think it works.What is the different between NH2+ and NH3
for ammoniation (the gromacs ask to choose one of them)? also a
I did a similar task. You should know the parameters and convert your files
format to gromacs format. A bit difficult but possible.
On Sun, Aug 9, 2015 at 9:35 PM, Justin Lemkul wrote:
>
>
> On 8/9/15 12:59 PM, mohammad r wrote:
>
>> Thank you MaryamI want to use this force field in the first s
On 8/9/15 12:59 PM, mohammad r wrote:
Thank you MaryamI want to use this force field in the first step of generating
the topology file (pdb2gmx command in the force field shown after this
command). Is it possible? and unfortunately I don't know how to find the
necessary files of this force f
Thank you MaryamI want to use this force field in the first step of generating
the topology file (pdb2gmx command in the force field shown after this
command). Is it possible? and unfortunately I don't know how to find the
necessary files of this force field. I searched a lot but I didn't succee
let me modify my previous message: in the g_x2top command, not grompp :-)
On Sun, Aug 9, 2015 at 8:14 PM, Maryam Kowsar
wrote:
> Hi Mohammad,
>
> Yes that's possible. You should just have the necessary files of your
> desired forcefield(.atp,.itp,...), and put them in a folder. in the grompp
> c
Hi Mohammad,
Yes that's possible. You should just have the necessary files of your
desired forcefield(.atp,.itp,...), and put them in a folder. in the grompp
command just add -ff folder name. that's all! It will use your forcefield
instead of the present forcefields in gromacs.
Regards,
-Maryam
Hi;
I want to use ff14SB Amberprotein force field. But it isn't included in the
gromacs force fields list.Is it possible to use this force field? How can I add
it in?Thank you, Mohammad.
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for
Molecular Biophysics
From:
gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of SAPNA
BORAH
Sent: Wednesday, August 05, 2015 10:20 AM To:
gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias???
Dear all,
Thank you for your answers which definitely cl
ck,
>>
>> Micholas
>>
>> === Micholas Dean Smith, PhD. Post-doctoral Research
>> Associate University of Tennessee/Oak Ridge National Laboratory Center for
>> Molecular Biophysics
>>
>> From:
>> g
PNA BORAH
Sent: Wednesday, August 05, 2015 10:20 AM To:
gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias???
Dear all,
Thank you for your answers which definitely clears some of my doubts. I am
trying to unfold a lectin tetramer protein that comprises largely of beta
strands, and
users-boun...@maillist.sys.kth.se
on behalf of SAPNA BORAH
Sent: Wednesday, August 05, 2015 10:20 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Force-field bias???
Dear all,
Thank you for your answers which definitely clears some of my doubts. I am
trying to unfold a lectin tetramer protein that
> Center for Molecular Biophysics
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin
> Lemkul
> Sent: Wednesday, August 05, 2015 7:31 AM
> To: gmx-us...@gromacs.org
> Subject: Re:
: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Force-field bias???
On 8/5/15 6:24 AM, SAPNA BORAH wrote:
> Dear all,
>
> I have a general query about unfolding simulations. Is there a bias among
> force-fields selected for unfolding, i.e. is it possible that unfolding of
> the
On 8/5/15 6:24 AM, SAPNA BORAH wrote:
Dear all,
I have a general query about unfolding simulations. Is there a bias among
force-fields selected for unfolding, i.e. is it possible that unfolding of
the protein may be different with a change in force fields applied?
Literature has given some sup
I believe, yes, it can. Dihedrals can make a big difference...
On Wed, Aug 5, 2015 at 7:24 AM, SAPNA BORAH wrote:
> Dear all,
>
> I have a general query about unfolding simulations. Is there a bias among
> force-fields selected for unfolding, i.e. is it possible that unfolding of
> the protein
Dear all,
I have a general query about unfolding simulations. Is there a bias among
force-fields selected for unfolding, i.e. is it possible that unfolding of
the protein may be different with a change in force fields applied?
Literature has given some support on this, however, I am not sure how t
Dear Farideh,
We have recently published an article on PAMAM dendrimers. We used oplsaa
forcefield. You can access the paper at
http://pubs.rsc.org/en/content/articlelanding/2015/sm/c5sm00854a.
Hope it helps.
Chandan
On Mon, May 18, 2015 at 12:58 PM, faride badalkhani <
farideh.kham...@gmail.co
Dear all,
I want to perform MD simuations on PAMAM dendrimers, but unfortunately this
molecule has not been defined in any of the GROMACS force fields.
Therefore, I should parameterize the force field for my purpose. How should
I do this procedure?
(It is mentionable that I read the
http://www.gro
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