Hi Bikash,
You can use a Charmm membrane with an Amber topology. The AA atom orders
are the same, AFAIK. For what it's worth, you can generate membranes
quickly using the coarse-grain command-line tool insane and (after
equilibration) convert the result to AA with the backmapping tool backward.
C
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Hi Catarina
Thanks for your reply, I really appreciate it. you know, I complete
Justin's Tutorial, so I know what procedures I should do. but now I
want to embed 2rh1
Hi Catarina
Thanks for your reply, I really appreciate it. you know, I complete
Justin's Tutorial, so I know what procedures I should do. but now I
want to embed 2rh1 protein into DPPC lipid bilayer� which I already
downloaded it from rcsb.com.� when I tried to use pdb2gmx� vi
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Dear justin
after finishing your tutorial, I tried to embed 1r2h protein into lipid
bilayer. when I tried to use pdb2gmx� via "gmx pdb2gmx -f
2rh1.pdb -o 2rh1_processe
Hello friends,
I want to dock a simulated protein like: human serum albumin to the drug. I was
wondering if i could use docking with gromacs or other softwares?If I can use
gromacs docking, where can i find a good tutorial ?
thank you,Negar.Parvizi
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Dear Gromacs user,
In my NVT simulation, I user the Verlet as cutoff-scheme, but below note
comes up in screen while .tpr generation;
"Removing all charge groups because cutoff-scheme=Verlet"
Does it mean that the atoms which I have indicated a charge for them in
.top file will be removed? or wh
Hi,
You might want to read this:
http://www.gromacs.org/Documentation/Cut-off_schemes
Basically, in the past Gromacs kept track of interactions through the group
scheme (which made use of charge groups). The more recent verlet scheme
doesn't use charge groups - that's what that line is telling yo
Dear Gromacs users,
I have performed PMF calculation for my system in water at npt, I ran them on
GPU .
Now I wish to run them in gas phase and compare them with the waters and I have
some questions:
To run in gas I should place pbc=no rlist=rcoulomb=rvdw=0. The GPU only support
the cutoff-
Maybe try this one instead:
https://github.com/gromacs/regressiontests/archive/release-5-1.zip
Cheers,
João
On Sat, Feb 20, 2016 at 6:27 AM, ikrormi rungsung
wrote:
> Hi,
>
> I couldn't download REGRESSIONTESTS-5.1.tar.gz from this
> sitegerrit.gromacs.org/download/regressiontests-5.1.tar.gz.
On 2/20/16 1:59 AM, Timofey Tyugashev wrote:
I was looking for examples of calculation setups. So I have a couple of
questions about one used in this paper
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123984#sec008
Parameters are amber99sb-ildn and gaff:
"Simulations were c
Please don't spam the list with many copies of the same message. People give of
their free time to answer questions on the list, so it may take a while for
someone to respond. Please also make sure your emails are legible; yours are
littered with bizarre characters.
On 2/20/16 5:30 AM, kho
On 2/20/16 7:03 AM, Negar Parvizi wrote:
Hello friends,
I want to dock a simulated protein like: human serum albumin to the drug. I was
wondering if i could use docking with gromacs or other softwares?If I can use
gromacs docking, where can i find a good tutorial ?
GROMACS doesn't perform d
On 2/20/16 8:49 AM, mohammad r wrote:
Hi Justin,
Thank you for your answer, I used grompp and it didn't give me error. I've
attached a topology file of my systems. Can you please take a look at this and
tell me your opinion? You mean that it doesn't make any problem when after
conversion proce
Please be sure to keep the discussion on the mailing list.
On 2/20/16 8:54 AM, Sana Saeed wrote:
thank you for explaining. i studied manual and understood restraints. but i
don't know how to get phi dphi and other parameters, is there any formula or
tool to get these values.
phi = the value y
On 2/20/16 1:49 PM, Rasha Alqus wrote:
Dear Gromacs users,
I have performed PMF calculation for my system in water at npt, I ran them on
GPU .
Now I wish to run them in gas phase and compare them with the waters and I have
some questions:
To run in gas I should place pbc=no rlist=rcoulom
Hi Bikash,
yeah, you can try CharmmGui. If it fails to create this small system,
you can use our MembraneEditor with the Packing Algorithm Distributer
and define the number of lipids you want to have. You will have to check
which membrane size you want. Just check the are per lipid.
Get here
Hi all,
I need to extend a previous simulation, and its directory is the same with
all inputs and outpts. That simulation can not be complete due to the
maximum time of the job which is limited by the server. I use gromacs 5,
when using the command gmx convert-tpr, an error is obtained.
Command
Hi, Justin,
Thanks for your response. By extracting temperature information out edr
file, do you mean the "gmx enemat" command? Actually what I was up to is
calculate the temperature development of a certain region instead of a
group of atoms.
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Hi,
You need to provide a number of ps by which you wish to extend, not the
text "timetoextendby"
Mark
On Sat, 20 Feb 2016 21:55 Elsaid Younes wrote:
> Hi all,
>
> I need to extend a previous simulation, and its directory is the same with
> all inputs and outpts. That simulation can not be co
On 2/20/16 3:58 PM, Ray Chao wrote:
Hi, Justin,
Thanks for your response. By extracting temperature information out edr
file, do you mean the "gmx enemat" command? Actually what I was up to is
No, you need gmx energy.
calculate the temperature development of a certain region instead of a
The simulation has the time, which is time of the wanted simulation.
But the job was killed by the server.
/Elsaid
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On 2/20/16 5:32 PM, Elsaid wrote:
The simulation has the time, which is time of the wanted simulation. But the
job was killed by the server.
If the simulation terminated prior to completion, you don't need to operate on
the .tpr file at all. Just continue from the last checkpoint
mdrun -
Hi,
If I have this file md_0_1_prev.cpt What is the text exactly? It asks
for topol.tpr
On 2/20/16 5:32 PM, Elsaid wrote:
>* The simulation has the time, which is time of the wanted simulation. But the
*>* job was killed by the server.
*
If the simulation terminated prior to completion, you don'
On 2/20/16 6:49 PM, Elsaid Younes wrote:
Hi,
If I have this file md_0_1_prev.cpt What is the text exactly? It asks
for topol.tpr
I gave you the command-line options that are new to the mdrun command line. Run
whatever mdrun you did before, but add -cpi -append. Doing this is a routine
t
Still asks for topol.tpr? Can I have that file
/Elsaid
On 2/20/16 6:49 PM, Elsaid Younes wrote:
>* Hi,
*>>>* If I have this file md_0_1_prev.cpt What is the text exactly? It asks
*>* for topol.tpr
*
I gave you the command-line options that are new to the mdrun command
line. Run
whatever mdrun yo
On 2/20/16 7:43 PM, Elsaid Younes wrote:
Still asks for topol.tpr? Can I have that file
You already have a .tpr file, otherwise your simulation never would have run.
If you want help, you need to provide (1) the exact mdrun you gave originally
for the job that stopped prematurely and (2) t
Hi,
The mdrun I did was gmx mdrun -deffnm md_0_1
I write the command
mdrun -cpi md_0_1_prev.cpt -append
I tried to use -noappend, but still doesn't work.
/Elsaid
On Sun, Feb 21, 2016 at 2:43 AM, Elsaid Younes wrote:
> Still asks for topol.tpr? Can I have that file
>
>
> /Elsaid
> On 2/20/16
On 2/20/16 7:59 PM, Elsaid Younes wrote:
Hi,
The mdrun I did was gmx mdrun -deffnm md_0_1
I write the command
mdrun -cpi md_0_1_prev.cpt -append
I tried to use -noappend, but still doesn't work.
To quote myself from my previous message:
"Run whatever mdrun you did before, but add -cpi
Ok, How can I use md_0_1.tpr instead of topol.tpr
/Elsaid
On Sun, Feb 21, 2016 at 2:59 AM, Elsaid Younes wrote:
> Hi,
>
> The mdrun I did was gmx mdrun -deffnm md_0_1
> I write the command
> mdrun -cpi md_0_1_prev.cpt -append
> I tried to use -noappend, but still doesn't work.
>
> /Elsaid
>
>
On 2/20/16 8:21 PM, Elsaid Younes wrote:
Ok, How can I use md_0_1.tpr instead of topol.tpr
Your original command:
gmx mdrun -deffnm md_0_1
"Run whatever mdrun you did before, but add -cpi -append."
which means:
gmx mdrun -deffnm md_0_1 -cpi -append
-Justin
/Elsaid
On Sun, Feb 21, 201
Hi,
Please do exactly what Justin has suggested twice :-)
Mark
On Sun, 21 Feb 2016 02:21 Elsaid Younes wrote:
> Ok, How can I use md_0_1.tpr instead of topol.tpr
>
> /Elsaid
>
> On Sun, Feb 21, 2016 at 2:59 AM, Elsaid Younes wrote:
>
> > Hi,
> >
> > The mdrun I did was gmx mdrun -deffnm md_0_
It says:
No previous checkpoint file present, assuming this is a new run.
Reading file md_0_1.tpr, VERSION 5.0.4 (single precision)
Changing nstlist from 10 to 20, rlist from 1 to 1.03
then start..
/Elsaid
On Sun, Feb 21, 2016 at 3:21 AM, Elsaid Younes wrote:
> Ok, How can I use md_0_1.tp
Sorry
Once, I added .tpr to the md_0_1 then it gave me the above message then I
did as you said without .tpr.
That error was obtained:
Fatal error:
Can't read 509132 bytes of 'md_0_1.log' to compute checksum. The file has
been replaced or its contents have been modified. Cannot do appending
becaus
On 20/02/2016 1:02 pm, gromacs.org_gmx-users-requ...@maillist.sys.kth.se
wrote:
Re: Regarding Lipid bilayer genration (Bikash RanjanSahoo)
Just a remark: please note that you are free in the choice of the force
field if you use the MembraneEditor. I used ffG45a3 and ffG53a6 without
problems
Dear Gromacs experts,
Is there a approach to fix the centre of mass of a group of atoms only without
fixing all of the atoms during a stretching process?
Regards,
Ming
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Hi,
Is there a way to generate position restraint files such that the main chain
atoms and the side chain atoms have different force constants? Similarly, would
it be possible to constrain atoms with B-factors lower than a certain threshold?
Best,
Irem
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