Hi,
Actually you have already applied pbc,and there seems nothing wrong.
Some atoms are out of the box is common.
If your box vector is correct,then Gromacs will run successfuly afterwards.
At 2013-04-03 22:51:54,Abhinav Agrawal abhv.a...@gmail.com wrote:
Hi,
I have a polymer box on which I wish
Dear all,
We are stuck at the last stage of running a successful REMD.
We have obtained average potential energy by fitting the energy values from
initial MD.
We want to get the temperature spacing for 72 replicas, starting from 280K.
We have gone through numerous papers, but none of them explain
Dear Friends,
I simulated the 4 peptide in water box .
As they come close to each other they start to from anti-parallel
beta sheet structure.
Now I want to draw the Free energy surface for the
same ..How is there pot energy ???
Would you please tell me how to do it ..
( I read about
Dear Gromacs users,
a)I wish to probe the change in electrostatic potential around a residue/
a group of residues throughout the trajectory. Will the g_potential output
be reliable in this regard?
b) Is there any way available to probe the change in energy associated
with a residue upon the
Dear
http://folding.bmc.uu.se/remd/ this may help you.
With best regards
On Thu, Apr 4, 2013 at 11:43 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com
wrote:
Dear all,
We are stuck at the last stage of running a successful REMD.
We have obtained average potential energy by fitting the
Dear GMX users,
I am working on a protein which I want to simulate in a lipid bilayer
environment (POPC) and want to use OPLS force field for the same. I have
previously rum the membrane protein simulations using 43a6 force field with
the help of justin's tutorial which had run quite fine. But I
Hi,
After applying energy minimization most of the atoms leave the box ( around
95%).
I am using a composite system of polymer and clay. The composite box (5.8
nm * 5.8 nm *7 nm) is made from combining a polymer box (5.7 nm * 5.7 nm *
5.7 nm) and clay box (5.5 nm * 5.1 nm * 1 nm) using editconf
On 4/3/13 9:46 PM, Abhinav Agrawal wrote:
Hi,
I have a polymer box on which I wish to apply energy minimization.
However,
when I do energy minimization runs to polymer chain unravels and goes out
of the box. I guess this is because periodic conditions are not applied.
My em.mdp file is:
On 4/3/13 11:03 PM, mu xiaojia wrote:
Thanks Justin,
It never happens to my simulations before, is there anyway to figure out
what caused this corruption? the log file and screen outputs didn't
mentioned any error message. I am wandering if it was caused by the
unstable super-cluster I am
Thanks for that link.
I have used it, but it only takes system size properties. It doesn't take
the potential energy values at all.
I am looking if someone has used any alternate for temperature spacing
generation?
On Thu, Apr 4, 2013 at 1:16 PM, rama david ramadavidgr...@gmail.com wrote:
Dear
On 4/4/13 3:56 AM, Parul tew wrote:
Dear GMX users,
I am working on a protein which I want to simulate in a lipid bilayer
environment (POPC) and want to use OPLS force field for the same. I have
previously rum the membrane protein simulations using 43a6 force field with
the help of justin's
On 4/4/13 12:27 AM, Kavyashree M wrote:
Sir,
That is true, previously you had explained regarding this.
Calculation using g_saltbr
1. For g_saltbr I included the following residues -
ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated
which contained only these residues. sb
On 4/4/13 2:14 AM, rama david wrote:
Dear Friends,
I simulated the 4 peptide in water box .
As they come close to each other they start to from anti-parallel
beta sheet structure.
Now I want to draw the Free energy surface for the
same ..How is there pot energy ???
Would you please
Sir,
Why I mentioned NH2 CG saltbridge because the g_saltbr
gives the charge group and does not mention the OD2 of ASP
but mentions only CG. Otherwise it does not make any sense.
Thanks
Regards
Kavya
On Thu, Apr 4, 2013 at 1:53 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/4/13 12:27 AM,
Hey :)
I'll make a try to be a bit more constructive :p
First of all, always try to think out of the box, especially with PBC :D
The problem may be due to overlapping atoms/molecules, pushing each other
out during energy minimization. When merging boxes, be careful not to
introduce overlaps, by
On 4/4/13 4:34 AM, Kavyashree M wrote:
Sir,
Why I mentioned NH2 CG saltbridge because the g_saltbr
gives the charge group and does not mention the OD2 of ASP
but mentions only CG. Otherwise it does not make any sense.
Now I remember how g_saltbr naming works. It measured distances between
I have a clay pdb file
http://s24.postimg.org/je3mvov9h/MMT.png
and a polymer structure file:
http://s24.postimg.org/ei003zv45/PLA.png
I use the following commands to generate a composite box
genbox -cp mmt.pdb -o mmt_box.gro
editconf -f mmt_box.gro -o mmt_newbox.gro -box 5.800 5.811 7.5
Dear gmx-users, dear Mark,
thank you for all the help you are giving me for this subject. I'm still
proceeding to my target..
Thanks to your previous suggestions, I was able to parametrize bonds and
angles of CFY. Now I'm dealing with dihedrals...
In the parameter files derived by Antechamber
Thank you justin,
I read the articles, archive and also g_sham -h,
As I mentioned in previous mail, I simulated four random coil peptide ,
they started to form
Beta sheet structure after 20 ns ..( simulation time 100ns )
My interest is how to draw the Free energy diagram for Potential energy
Ok. Still the distance is beyond the mentioned
cut-off. The distance of both OD1 and OD2 of
ASP is more than 4 Ang from NH2 of Arg.
Thank you
Regards
Kavya
On Thu, Apr 4, 2013 at 2:25 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/4/13 4:34 AM, Kavyashree M wrote:
Sir,
Why I mentioned
So let me see if I understood what Francesco said correctly. Restarting a
REMD job after hitting the cluster wall-time limit resets the information
stored in the log files? Can someone shed some light on this subject?
Best regards,
João Henriques
--
gmx-users mailing listgmx-users@gromacs.org
This is what I meant,
in particular it is a problem when I want to analyze
the data regarding the exchange probability.
Francesco
2013/4/4 João Henriques joao.henriques.32...@gmail.com
So let me see if I understood what Francesco said correctly. Restarting a
REMD job after hitting the cluster
That's terrible! I was just about to restart 2 hefty REMD simulations...
Maybe I can move the original log files somewhere and combine them with the
restart ones afterwards by using a script. It's just an idea, because I
need to run Demux.pl on the final concatenated log file.
Any other issues I
Hey Abhinav,
Your polymer seems to be one long molecule, which is made whole over PBC.
The result has nothing to do with EM.
Cheers,
Tsjerk
On Thu, Apr 4, 2013 at 11:37 AM, Abhinav Agrawal abhv.a...@gmail.comwrote:
I have a clay pdb file
http://s24.postimg.org/je3mvov9h/MMT.png
and a
if your -append option is activated (the default is yes),
maybe Demux.pl reads the exchanging from the .log taking into account the
time in the
log and so you don't need to do anything.
But I don't know how Demux.pl works :(
Francesco
2013/4/4 João Henriques joao.henriques.32...@gmail.com
Sorry to bother you all once again. As there were no replies, I assume it is
not possible to implement COM distance restraints in a way similar to distance
restrains.
nahren
From: nahren manuel meetnah...@yahoo.com
To: gromacs gromacs gmx-users@gromacs.org
On 4/4/13 5:18 AM, Kavyashree M wrote:
Ok. Still the distance is beyond the mentioned
cut-off. The distance of both OD1 and OD2 of
ASP is more than 4 Ang from NH2 of Arg.
The cutoff is applied per group, not per atom within the group, IIRC. So if the
charge group at any time comes closer
On 4/4/13 5:50 AM, rama david wrote:
Thank you justin,
I read the articles, archive and also g_sham -h,
As I mentioned in previous mail, I simulated four random coil peptide ,
they started to form
Beta sheet structure after 20 ns ..( simulation time 100ns )
My interest is how to draw the
It is, and I think there was in fact some experimental/private branch that
dabbled with this. It hasn't gone into the official releases yet and there is
no guarantee that it will.
Erik
On 4 Apr 2013, at 14:10, nahren manuel meetnah...@yahoo.com wrote:
Sorry to bother you all once again. As
Thank you a lot justin for offering me help.
I am interested to use g_sham ..( And if the other command give me my
output, I am also interested to know the other way )
I was confuse with the input that I have to give with g_sham.
I proceed the following command
g_energy is used to get
On 4/4/13 9:37 AM, rama david wrote:
Thank you a lot justin for offering me help.
I am interested to use g_sham ..( And if the other command give me my
output, I am also interested to know the other way )
I was confuse with the input that I have to give with g_sham.
I proceed the following
Justin Lemkul wrote
On 4/3/13 11:13 AM, Oleksandr Sushko wrote:
Dear Gromacs users,
can you help me please with next issue:
I'm analysing solvation shell of water molecules around a protein.
I use g_select to select different layers of water based on distance
criteria.
The output index file
There's no simple answer for that. If you apply a lateral pressure (xy
plane) and the system is evacuated in the z direction, the only thing that
you might expect is that your system would be squeezed in that direction,
and then the lateral pressure would relax.
If you're thinking about a gas
Hello Fellow Users,
I have a question regarding US simulation.
I am interested to know that can I treat hydrogens as virtual sites in US
simulations??
I have very large protein complexes and to use higher time stepping during
simulations...I am thinking to use -vsite option.
what do you guys
Dear all,
I am having trouble creating topology file for simple molecule ethylene.
Here is the steps. Below is the pdb file:
Ethylene.pdb:
ATOM 1 C1 ETY 1 0.672 -0.000 0.000 1.00 0.00
C
ATOM 2 C2 ETY 1 -0.672 -0.000 0.000 1.00 0.00
C
ATOM 3 H11
Dear Justin,
Thank you a lot for help and kind passion to listen me.
I finally come with the my desired out put.
I
I am grateful to you for help.
With Best Wishes,
Rama david
On Thu, Apr 4, 2013 at 7:09 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/4/13 9:37 AM, rama david wrote:
Dear Dr. Moura,
Thank you for your answer. I equilibrated the cell under NPT and then
extended the Z direction to get a surface. Since I run NVT and Z is
extended, I see no pressure dependence and surface tension values are
similar for all P from 50 to 1000 bar. which is attributed to the fact
Hi, i'm trying to run an MD simulation of a protein with a tRNA and i'm getting
an error that it does not recognize the modified residue H2U (DHU), i tried
changing the forcefield to one that was user contributed but didn't work
either. can anyone point me to some resource or tell he how you
Dear Richard,
I've included the COM in my .gro and also updated the rtp, atp and
ffnonbonded.itp files as well as the exact coefficient value. But when I use
gromp I get the error that COM not found in atom type database .
Actually I included the COM in atomtypes.atp like
COM 0.
As it
Please include the full error message and the grompp line you used when
asking for help. Without them I can't tell what you are doing.
Richard
On 04/04/2013 17:40, 라지브간디 ra...@kaist.ac.kr wrote:
Dear Richard,
I've included the COM in my .gro and also updated the rtp, atp and
ffnonbonded.itp
Is there a way to run more than one simulation with a single .mdp file? For
instance, if I want to do an equilibration run and then the actual
production run, do I have to make an input file for each run or can this be
done with a single file?
Thanks.
--
Tim Moore
--
gmx-users mailing list
On Apr 4, 2013 7:30 PM, Tim Moore tcmoo...@gmail.com wrote:
Is there a way to run more than one simulation with a single .mdp file?
No, unless you happen to be able to abuse the simulated annealing protocol.
Shell scripts are among your friends here.
Mark
For
instance, if I want to do an
I always do. There's nothing particular about umbrella sampling in this respect.
On 4 Apr 2013, at 17:33, raghav singh raghavbioi...@gmail.com wrote:
Hello Fellow Users,
I have a question regarding US simulation.
I am interested to know that can I treat hydrogens as virtual sites in US
Demux.pl pre-dates .cpt and -append. The only solution is to preserve your
.log files (e.g. with -noappend) and post-process. If you do that by
modifying demux.pl, please consider contributing your fix back.
Mark
On Apr 4, 2013 1:42 PM, francesco oteri francesco.ot...@gmail.com wrote:
if your
Dear Gromacs users,
I'd appreciate any help in rather strange problem.
I'm want to analyse stratified layers of water around protein,
so I provide next selection file to g_select:
*
**shell = group SOL and same residue as within 0.4 of group protein**;**
**shell1 = group SOL and same residue as
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Fieldhas
the standard workflow.
Mark
On Thu, Apr 4, 2013 at 6:25 PM, Juan Antonio Raygoza Garay raygo...@psu.edu
wrote:
Hi, i'm trying to run an MD simulation of a protein with a tRNA and i'm
getting an error that it
On Thu, Apr 4, 2013 at 11:40 AM, Anna Marabotti amarabo...@unisa.it wrote:
Dear gmx-users, dear Mark,
thank you for all the help you are giving me for this subject. I'm still
proceeding to my target..
Thanks to your previous suggestions, I was able to parametrize bonds and
angles of CFY. Now
On Thu, Apr 4, 2013 at 10:17 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com
wrote:
Thanks for that link.
I have used it, but it only takes system size properties. It doesn't take
the potential energy values at all.
Actually it does, inasmuch as it uses parameters fitted to observed energy
On Thu, Apr 4, 2013 at 7:57 AM, imsharmanitin k.nitin.sha...@gmail.comwrote:
i followed the following steps to install gromacs :
1. Download cygwin from http://www.cygwin.com/ .Installed packages
including
gdb, make and tcsh
NOTE : i was not able to find package gdn
2. Downloaded GROMACS
Looks nice :-) Python .edr reading would be particularly useful for some
kinds of analysis with existing Python tools. I'll see how well it works
sometime soon ;-)
Mark
On Wed, Apr 3, 2013 at 7:31 PM, Gabriele Lanaro
gabriele.lan...@gmail.comwrote:
Hello GMX users, I just wanted to share a
On 4/4/13 11:38 AM, Juliette N. wrote:
Dear all,
I am having trouble creating topology file for simple molecule ethylene.
Here is the steps. Below is the pdb file:
Ethylene.pdb:
ATOM 1 C1 ETY 1 0.672 -0.000 0.000 1.00 0.00
C
ATOM 2 C2 ETY 1 -0.672
Hi Justin,
Thanks a lot for your message. I am petrified why pdb2gmx is not
recognizing the residue ETY. This the first residue added to ffoplsaa.rtp
but as you may see below it is not read from rtp.
I am sure this residue is added to ffoplsaa.rtp which is existing in the
working directory:
[
On 4/4/13 6:17 PM, Juliette N. wrote:
Hi Justin,
Thanks a lot for your message. I am petrified why pdb2gmx is not
recognizing the residue ETY. This the first residue added to ffoplsaa.rtp
but as you may see below it is not read from rtp.
I am sure this residue is added to ffoplsaa.rtp which
53 matches
Mail list logo
