Thank you very much from your time.
Best Regards
Sara
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Friday, October 5, 2012 9:48 AM
Subject: Re: [gmx-users] equilibrium for box of simulation
On 5/10/2012 4:12 PM, mohammad agha wrote:
> Dear
On 5/10/2012 4:12 PM, mohammad agha wrote:
Dear Mark,
Yes, you're right. Excuse me, for this and thank you for your reminder.
May I know your idea about cause of my doubt, Please?
As I said yesterday:
At least one of your volume, contents or model physics are not
consistent with the others,
Dear Mark,
Yes, you're right. Excuse me, for this and thank you for your reminder.
May I know your idea about cause of my doubt, Please?
Best Regards
Sara
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Friday, October 5, 2012 9:34 AM
Subjec
On 5/10/2012 3:55 PM, mohammad agha wrote:
Dear Justin,
Thank you very much.
So, decreasing of box dimensions is not bad, if all thing process natural, yes?
The cause of my doubt was because of in the most of articles was said for example "
we select box with dimensions 10nm that after equilibr
Dear Justin,
Thank you very much.
So, decreasing of box dimensions is not bad, if all thing process natural, yes?
The cause of my doubt was because of in the most of articles was said for
example " we select box with dimensions 10nm that after equilibrium was
converted to 11nm" and I didn't see
On 10/4/12 5:56 PM, Elie M wrote:
I guess the first parameter of each pair is easy to find. what about kb? k
theta?. kb is the force constant isnt it? any reference about a method how
to calculate them please? pr anything atht might be of help.
Bonded parameters are generally based on
I guess the first parameter of each pair is easy to find. what about kb? k
theta?. kb is the force constant isnt it? any reference about a method how
to calculate them please? pr anything atht might be of help.
Elie
> Date: Thu, 4 Oct 2012 16:25:35 -0400
> From: jalem...@vt.edu
> To: gmx-u
On 10/4/12 5:29 PM, Bao Kai wrote:
Hi, all,
I am still working on the molecular simulation of CO2 and H2O mixture.
The information of the molecules types and the force field model are
all defined in the a.top file.
1 [ defaults ]
2 ; nbfunccomb-rule gen-pairs fudgeLJ fu
Hi, all,
I am still working on the molecular simulation of CO2 and H2O mixture.
The information of the molecules types and the force field model are
all defined in the a.top file.
1 [ defaults ]
2 ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
3 1 3 y
On 4/10/2012 3:37 PM, Deepak Ojha wrote:
Dear All
I want to use Amber force field in Gromacs therefore I installed the
latest version of Gromacs and
installed accordingly as per as the instructions given in INSTALL.automake file.
./configure
make
make install
It works fine and shows the message
On 5/10/2012 1:49 AM, lloyd riggs wrote:
Please choose descriptive subjects and start new email messages when
posting to mailing lists. This makes people better able to respond to
you by allowing mail reading software to work properly. Cross-posting to
the VMD and GROMACS lists when your quest
On 10/4/12 4:54 PM, Sonia Aguilera wrote:
Hi,
I am performing a free energy calculation based on Justin Lemkul's tutorial.
My system is a protein in water and dodecane and I'm coupling the protein
considering none to only vdw interactions for my lambda 0 and 1 states.
However, I get this error
Hi,
I am performing a free energy calculation based on Justin Lemkul's tutorial.
My system is a protein in water and dodecane and I'm coupling the protein
considering none to only vdw interactions for my lambda 0 and 1 states.
However, I get this error when trying to minimize the system:
Fatal e
On 10/4/12 4:22 PM, Elie M wrote:
I guess now I get what is happening finally. Correct me if I am wrong. The
.top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which
was also modified to include atoms that were not there *but present in
atomtypes.atp). The .top file describe
I guess now I get what is happening finally. Correct me if I am wrong. The
.top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which was
also modified to include atoms that were not there *but present in
atomtypes.atp). The .top file describes all the bonds and angles in the
On 10/4/12 1:12 PM, vidhya sankar wrote:
Dear Justin ,
Thank you for you Previous reply.
I am doing Simulation of Cyclic Peptide in Lipids I am following your
tutorial When I use inflategro script For my System I have got Output
System_inflated.gro file with certain
Dear Justin ,
Thank you for you Previous reply.
I am doing Simulation of Cyclic Peptide in Lipids I am following your
tutorial When I use inflategro script For my System I have got Output
System_inflated.gro file with certain message in Command prompt as follows .
Th
On 10/4/12 12:25 PM, mohammad agha wrote:
Dear Justin,
Thank you very much from your help.
Oh, yes, the vectors of box are downward in the first with much slope and then
the slope became milder and milder and then it become almost fix.
For checking of density, should I use from formula: d=m
On 10/4/12 12:13 PM, Elie M wrote:
Thanks a lot. I have sorted out the error that occured in the ffoplsaabon.itp; I have
commented ";" one line which was given the first two errors. Now the only
errors remaining are the bonds, angles and some others. How to correct these?
For example one of
Dear Justin,
Thank you very much from your help.
Oh, yes, the vectors of box are downward in the first with much slope and then
the slope became milder and milder and then it become almost fix.
For checking of density, should I use from formula: d=m/v?
Best Regards
Sara
- Original Messa
Thanks a lot. I have sorted out the error that occured in the ffoplsaabon.itp;
I have commented ";" one line which was given the first two errors. Now the
only errors remaining are the bonds, angles and some others. How to correct
these?
For example one of them is (the error occuring at line 11
Hello Everybody,
I am using g_covar with -xpmc flag in-oder to generate matrix of
atomic correlation coefficients. At present I am using g_covar script
given by Ran, which I downloaded from gromacs user modified script
pool.
Since Ran's script is for gromacs 3.3.3 and it not accept .trp input
fro
Dear All,
I spent two days converting a .top file from gromos53a6 to one readable by
VMD/NAMD.
Now I am about to begin the ffbonded/nonbonded to a readable format for the
same and would like to know beforehand if anyone has already done this so I can
just use the library? Most are straightfo
Please keep the discussion on the gmx-users list.
On 10/4/12 11:28 AM, mohammad agha wrote:
Dear Justin,
Thank you very much from your help.
I don't know about "vectors trending downward, or do they converge"
You can plot box vectors from the .edr file. That will give you their values
and
You could use 'constraint' pull-mode instead of the 'umbrella' mode.
Than the distance would change gradually and you won't observe the
fluctuations in the distance.
greetings
thomas
Am 04.10.2012 16:58, schrieb gmx-users-requ...@gromacs.org:
On 10/4/12 10:52 AM, jiang wrote:
>Justin Lemkul
On 10/4/12 10:52 AM, jiang wrote:
Justin Lemkul wrote
On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote:
Hi Justin,
I used ~20 windows to sample ~2 nm pulling. I notice that the distance
between the complex being increased during the pulling but not gradually.
At the distance of 0-1nm, there ar
Justin Lemkul wrote
> On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote:
>> Hi Justin,
>>
>> I used ~20 windows to sample ~2 nm pulling. I notice that the distance
>> between the complex being increased during the pulling but not gradually.
>> At the distance of 0-1nm, there are 70 snapshots (the dist
On 10/4/12 10:38 AM, mohammad agha wrote:
Dear Justin,
"my materials are not placed in the smaller box" means if I select box with
dimensions 5.99 nm, space is low and insufficient for my molecules! but after equilibrate
the box become small.
Please define what you mean here. You start wi
Dear Mark,
So, when in the equilibrium stage, the box become small, there is one mistake
in my system?
I don't know where is my mistake!
Best Regards
Sara
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Thursday, October 4, 2012 5:48 PM
Sub
Dear Justin,
"my materials are not placed in the smaller box" means if I select box with
dimensions 5.99 nm, space is low and insufficient for my molecules! but after
equilibrate the box become small.
According what you said, when the box become smaller in equilibrium, there is
not mistake and
On 10/4/12 10:12 AM, Elie M wrote:
Hello everyone,
Justin, I have repeated the procedures without doing any changes and it does
seem that you were right about the broken file. However now I get a different
set of errors:
(1) ERROR 1 [file ffoplsaabon.itp, line 2692]: Incorrect number of ato
On 10/4/12 10:06 AM, mohammad agha wrote:
Dear GROMACS Users,
I asked this question before but I don't understand it!
I placed several materials in my box of simulation for example box with
6nm*6nm*6nm and my materials are not placed in the smaller box but when I
equilibrate my system, the
On 10/4/12 9:16 AM, rama david wrote:
Thank you for reply,
I read the recently published article in Biochemistry.
They worked on the same receptor that I am working.
( as I mention in my previous mail)
They used NAMD software and I am using gromacs.
They sliced the receptor binding site and
On 5/10/2012 12:06 AM, mohammad agha wrote:
Dear GROMACS Users,
I asked this question before but I don't understand it!
I placed several materials in my box of simulation for example box with
6nm*6nm*6nm and my materials are not placed in the smaller box but when I
equilibrate my system, the
Hello everyone,
Justin, I have repeated the procedures without doing any changes and it does
seem that you were right about the broken file. However now I get a different
set of errors:
(1) ERROR 1 [file ffoplsaabon.itp, line 2692]: Incorrect number of atomtypes
for dihedral (4 instead of 2 or
Dear GROMACS Users,
I asked this question before but I don't understand it!
I placed several materials in my box of simulation for example box with
6nm*6nm*6nm and my materials are not placed in the smaller box but when I
equilibrate my system, the box became smaller and temperature and pressu
Hi James,
The bilayers from the CHARMM-GUI can be converted into any force field
using a simple script. For a united-atom force field you will need to
remove the non-polar hydrogens, rename the atoms and possibly reorder
some of the atoms in the lipids.
As for other methods to build membrane
Thank you for reply,
I read the recently published article in Biochemistry.
They worked on the same receptor that I am working.
( as I mention in my previous mail)
They used NAMD software and I am using gromacs.
They sliced the receptor binding site and used the the solid support
to the binding
Hi,
packmol generates just coordinates (pdb format) for optimized packing
arrangements of whatever molecule you provide as input. It's up to you
to parameterize the resulting model. CHARMM-GUI has a library of
conventional (phospho)lipids and generates the input for CHARMM
equilibration of th
Dear Felipe,
thanks for advise. Does the Packmol software suitable for generation
coordinates of the bergers ( for gromos 56 ff) lipids ? As I know
CHARMM-GUI membrane builder is suitable for only CHARMM force field
lipids.
James
2012/10/4 Felipe Pineda, PhD :
> To generate starting (non-equilib
I don't think AutoDock and Vina are suitable for peptide docking. I would
first try the FlexPepDocking module of Rosetta which does ab initio folding
of the peptide on the receptor, while moving the side-chains of the protein
but leaves its backbone intact. Rosetta implements a knowledge-based
scor
On 10/4/12 8:40 AM, rama david wrote:
Thank you justin and franscisco,
I have practical data that claim that only a particular residue that is c
terminal residue is
involve in binding.
but when I generate the docking data other residues most of the time
comes to play.
I know the binding of
Thank you justin and franscisco,
I have practical data that claim that only a particular residue that is c
terminal residue is
involve in binding.
but when I generate the docking data other residues most of the time
comes to play.
I know the binding of natural ligand ( peptide ) and the position
On 10/4/12 1:34 AM, Nur Syafiqah Abdul Ghani wrote:
Hi Guys,
Need your help urgently.
I already read a lot of paper about molecular dynamics simulation
which relate work as mine.The main point is to create the mix solvent.
The co-solvent is hexafluoroisopropanol and a lot of researcher cited
t
On 10/3/12 11:41 PM, shika wrote:
Thanks for fast reply.I am very new to this and yes I am confused
my itp file is :
; solvent_HFI.gro.top created by rdparm2gmx.pl Sat May 28 10:25:18 MYT 2005
;
;
[ moleculetype ]
; Namenrexcl
solute 3
[ atoms ]
; nr type
2012/10/4 rama david
> Hi francesco,
>
> Thank you For reply.
> I did docking but the result are not so impressive.
>
What does it mean "not so impressive"? I mean, do you have experimental
data
and the comparison with docking doesn't agree with experiments? Have you
generated
a sufficient numbe
On 10/4/12 8:08 AM, rama david wrote:
Hi francesco,
Thank you For reply.
I did docking but the result are not so impressive.
I used vina and autodock.
I also did virtual screening in autodock but the result are not upto the
mark.
Is the freezing of group can affect my system?? How much effici
Hi francesco,
Thank you For reply.
I did docking but the result are not so impressive.
I used vina and autodock.
I also did virtual screening in autodock but the result are not upto the
mark.
Is the freezing of group can affect my system?? How much efficiency I get
by these work??
As these group
Hi,
as far as I know, freezing just set velocities to 0 so you gain nothing
freezing atoms.
By the way, have you tried docking? It takes into account multiple
conformation and
orientation of the peptide and, depending upon the implemented algorithm,
also
protein sidechain orientation.
Francesco
thank you Justin for reply.
I dont know about long range interactions.
But as I freeze the group I think it will improve my computational speed.
So is there any way to find out or decide which group should be
freeze, and which group should affect my interaction most probably??
Should I do Essenti
On 10/4/12 2:01 AM, rama david wrote:
Hi gromacs Friends,
I want to do peptide-receptor ( Protein) interaction
study.Receptor consist a single chain.
Peptide is made up of 4 amino acids. I know the interaction pattern of
peptide and receptor.
I plan to mutate single residue each
Dear all,
I am using the pull code in Gromacs 4.5.5 to constrain the distance in one
direction (z) between a small molecule and a lipid bilayer. I run separate
simulations with distances 0-4 nm constrained. I use pull_geometry = cylinder.
The pull parameters are the following:
pull
Hi Rama,
I bet that wasn't the only output you got. Two things can usually
happen with do_dssp. Either you chose the wrong group for analysis, or
there is a problem with the version of DSSP. Probably the latter: DSSP
syntax changed recently, and I think that GMX 4.5.5 can't deal with
that. There s
So I have spent the past few weeks debugging my equilibration protocols,
which were an odd hybrid of examples ranging from GROMACS 3.3 up to GROMACS
4.5. I have cleaned out old code. I added an in vacuo energy minimization
step for the protein without solvent, and a missing NVT step after solvent
On 4/10/2012 5:10 PM, Albert wrote:
hello:
I found that the .trr from mdrun output is really much huger than
the .xtc file. However, most people would like to generate the .trr
file and then convert it into .xtc file.
See
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_St
Hello Albert,
Yes, the settings you mentioned will give you .trr and .xtc files during mdrun.
But please watch out, you have a little spelling typo in your message. It is
nstxtcout.
Cheers,
Felix
-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gro
On 10/04/2012 09:22 AM, rama david wrote:
Yes -x option ( please see mdrun -h )
You have to specify it as the output is optiona l
if you use -deffnm all the output posses the same name ( generally I do
these one )
set the mdp file option properly to get appropriate saving for xtc
( see
the m
To generate starting (non-equilibrated) bilayer structures for use in MD
simulations take a look at http://www.ime.unicamp.br/~martinez/packmol/.
Otherwise, for conventional lipids CHARMM-GUI membrane builder
(http://www.charmm-gui.org/?doc=input/membrane).
Hope it helps!
Felipe
On 10/04/201
hello:
I found that the .trr from mdrun output is really much huger than the
.xtc file. However, most people would like to generate the .trr file and
then convert it into .xtc file. I am just wondering can we generate the
.xtc file directly from mdrun command like:
mdrun -s md.tpr -o md.xt
On 2012-10-04 04:39, Nur Syafiqah Abdul Ghani wrote:
Dear Users,
Right now i already done for creating the a gro file from antechamber
to gromacs format of my molecule which is hexafluoroisopropanol.
But when i want to minimize it in vacuum it show atomtype F not found.
Im using oplsaa force fie
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