Hi All,
I am running a membrane protein MD simulation with Gromacs 5.1.4. I want to
add some substrate molecules(acetate) to my system, and I used this command:
"gmx insert_molecules -f ###.pdb(include the ptotein, POPC, etc.) -ci act.pdb
-o ###.pdb -nmol 48 -box 6.7 6.7 8.1 -try 500 -rot xy
- Message from Dilip H N -
Date: Tue, 4 Apr 2017 10:18:23 +0530
From: Dilip H N
Reply-To: gmx-us...@gromacs.org
Subject: [gmx-users] Regarding getting trajectories in gromacs..
To: gromacs.org_gmx-users@maillist.sys.kth.se
Hello,
I have ran a md simulation for
nsteps
Dear Gromacs users ,
I have a xyz file and I used OBGMX ( topology generator ) for that .
Now I have itp and top file , but the problem is I want to change UFF
forcefield ( that used by obgmx ) to gromacs forcefields like Amber03 .
Can you please let me know how can i do that ?
I am new in Groma
Hello,
I have ran a md simulation for
nsteps = 500 ; 2 * 500 = 1 ps (10 ns)
dt = 0.002 ; 1e+07 fs
nstxout= 5000 ; save coordinates every 20.0 ps
nstvout= 5000 ; save velocities every 20.0 ps
nstenergy= 5000 ; save energies every 20.0 ps
nstlog= 5000 ; update log file eve
Hi,
I’m continuing a run and setting init-step as the total steps completed in
the run i’m continuing from,
if I change the dt for the continuation do I need to scale the steps previously
taken? i.e going from dt = 1
to dt =2, completing 100 steps in the first sim, does init-step take the val
>> Hi,
>>
>> I?m receiving a couple (~15) EM did not converge warnings as well as a few
>> (~3) 1,4 interaction
>> warnings during my run. It looks like it starts down the path to blowing up
>> but recovers. Is this ?recovery?
>> system dependent? Should I take these messages (even without th
> Such a short dt and strict niter should not be necessary in practice. The
> failure of SCF to converge/LINCS warnings is what we typically refer to as
> polarization catastrophe, so your system is on the brink of instability.
> This
> is one of the inherent problems of SCF in polarizable s
Thank you. So if the below is correct, and it will run for 100 ns?
convert-tpr -s previous.tpr -extend 10 -o next.tpr
gmx mdrun -deffnm next -cpi previous.cpt
-- Original --
From: "Justin Lemkul";;
Date: Tue, Apr 4, 2017 02:12 AM
To: "gmx-users";
Subj
On 4/3/17 2:07 PM, ZHANG Cheng wrote:
(Following Justin's suggestion)
Dear Gromacs Researchers,
My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to
extend it to 100 ns.
As shown on
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
Should I use th
Hi,
Back up your files and try it :-) You will see that mdrun refuses to append
if you change -deffnm. So either don't append or don't change the name.
Mark
On Mon, Apr 3, 2017 at 8:09 PM ZHANG Cheng <272699...@qq.com> wrote:
> (Following Justin's suggestion)
>
>
> Dear Gromacs Researchers,
> M
(Following Justin's suggestion)
Dear Gromacs Researchers,
My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to
extend it to 100 ns.
As shown on
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
Should I use the following two lines of code for the fil
On 4/3/17 2:01 PM, Dan Gil wrote:
Thank you Dr. Lemkul,
I am trying to run grompp with the md integrator, but I am getting this
error:
"For proper sampling of the (nearly) decoupled state, stochastic dynamics
should be used"
Should I ignore this warning with the -maxwarn option and try runnin
Thank you Dr. Lemkul,
I am trying to run grompp with the md integrator, but I am getting this
error:
"For proper sampling of the (nearly) decoupled state, stochastic dynamics
should be used"
Should I ignore this warning with the -maxwarn option and try running it? I
will see if I obtain comparabl
On 4/3/17 1:42 PM, Dayhoff, Guy wrote:
Hi,
I’m receiving a couple (~15) EM did not converge warnings as well as a few
(~3) 1,4 interaction
warnings during my run. It looks like it starts down the path to blowing up but
recovers. Is this “recovery”
system dependent? Should I take these mes
On 4/3/17 1:41 PM, ZHANG Cheng wrote:
Dear Gromacs Researchers,
My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to
extend it to 100 ns.
As shown on
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
Should I use the following two lines of code for
Hi,
I’m receiving a couple (~15) EM did not converge warnings as well as a few
(~3) 1,4 interaction
warnings during my run. It looks like it starts down the path to blowing up but
recovers. Is this “recovery”
system dependent? Should I take these messages (even without the subsequent
crash)
Dear Gromacs Researchers,
My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to
extend it to 100 ns.
As shown on
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
Should I use the following two lines of code for the files in the same folder?
grompp -f
ISHRAT
Thank you very much.
On Sun, Apr 2, 2017 at 11:50 PM, ISHRAT JAHAN wrote:
> Hi,
> You have to calculate the number of alcohol and water molecules in the box
> and use genbox command with -nmol option.In -nmol put number of alcohol
> molecule and from the output of genbox command remove th
Hi,
Offhand, gen-pairs won't work without matching pairtypes, but
nonbond_params will override anything that might have been looked up from
pairtypes.
Mark
On Mon, Apr 3, 2017 at 2:39 PM Vries, de, H.W. <
h.w.de.vrie...@student.rug.nl> wrote:
> Dear all,
>
> I was wondering: what priority does
Dear all,
I was wondering: what priority does GROMACS use for comparing
[nonbond_params], [pairtypes], and gen-pairs-based cross-terms?
I.e., are pairtypes additive to gen-pairs, with nonbond_params overwriting
any cross-term defined through cross-terms?
The reason I am asking is that I am curre
Dear Justin,
Thanks for your kind help!
Best regards,
Sudip
On Mon, Apr 3, 2017 at 5:20 PM, Justin Lemkul wrote:
>
>
> On 4/1/17 1:18 AM, Sudip Das wrote:
>
>> Dear All,
>>
>> While I am preparing my system topology with pdb2gmx for a system
>> containing enzyme with 30 non-ionic surfactant
Hi,
Look at your docking result before you use it for something else. (Same
goes for any computed result from any software.)
Mark
On Mon, 3 Apr 2017 14:06 RAHUL SURESH wrote:
> The ligand is out of protein in the very first frame of production run.
> Then that should be my docking error.?
>
>
On 4/3/17 8:05 AM, RAHUL SURESH wrote:
The ligand is out of protein in the very first frame of production run.
Then that should be my docking error.?
It sounds like your starting configuration was prepared incorrectly (however you
manipulated it to prepare the system) or this is a PBC effe
The ligand is out of protein in the very first frame of production run.
Then that should be my docking error.?
On Mon, 3 Apr 2017 at 5:30 PM, Justin Lemkul wrote:
>
>
> On 4/3/17 7:56 AM, RAHUL SURESH wrote:
> > Dear Justin
> >
> > First I apologise for the error I had made in my previous mail.
On 4/3/17 7:56 AM, RAHUL SURESH wrote:
Dear Justin
First I apologise for the error I had made in my previous mail. It's during
production.
I have recentered it. The ligand is out of the protein. The ligand is not
in position where I docked.
Then watch the recentered trajectory to see what
Dear Justin
First I apologise for the error I had made in my previous mail. It's during
production.
I have recentered it. The ligand is out of the protein. The ligand is not
in position where I docked.
On Mon, 3 Apr 2017 at 5:21 PM, Justin Lemkul wrote:
>
>
> On 4/1/17 8:59 AM, RAHUL SURESH w
On 4/3/17 2:23 AM, Vytautas Rakeviius wrote:
MD can not simulate chemical reactions. What you can do prepare different forms
with acpype and compare all in some way.
External tools aren't even necessary. One just needs to select the proper
termini with pdb2gmx.
-Justin
On Monday,
On 4/1/17 8:59 AM, RAHUL SURESH wrote:
I followed the complex simulation tutorial. Minimisation for 2ns
FYI there is no time during energy minimization, so you did not do "2 ns" of
minimization.
I used auto dock to dock ligand with protein. During simulation I find the
ligand out of prot
On 4/1/17 1:18 AM, Sudip Das wrote:
Dear All,
While I am preparing my system topology with pdb2gmx for a system
containing enzyme with 30 non-ionic surfactant molecules in water, I got 36
number of bonds per surfactant molecules, but actually it has 37 bonds
(anyways, the number of angle, dihe
Hi,
Some of those tools calculate distribution functions. Please start by
looking at them and seeing if they seem suitable.
Mark
On Mon, Apr 3, 2017 at 11:59 AM ISHRAT JAHAN wrote:
> sorry i did not get what you said...
> actually i want to calculate distribution of water at various distance
>
sorry i did not get what you said...
actually i want to calculate distribution of water at various distance
around backbone as done in paper "Regulation and aggregation of
intrinsically disordered peptides" by Zachary A.Levine et.al.
On Mon, Apr 3, 2017 at 1:54 PM, Mark Abraham
wrote:
> Hi,
>
Hi,
If you ask for .trr output, you get it. Stop using non-zero nst*out mdp
settings that you don't want.
Mark
On Mon, Apr 3, 2017 at 11:31 AM Aman Deep wrote:
> sir,
>
> I have tried *nstxctout *but it still making trr file ... is there any
> option to make only xtc file ???
>
> On Mon, Apr
sir,
I have tried *nstxctout *but it still making trr file ... is there any
option to make only xtc file ???
On Mon, Apr 3, 2017 at 1:14 PM, Mark Abraham
wrote:
> Hi,
>
> See
> http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_
> Volume
>
> Mark
>
> On Mon, Apr 3, 2017
As you set smaller emtol you do better and longer minimization. So with 1000
you stop simulation way before polymer forms some rings. You can check video
with VMD Chimera or something.
On Saturday, April 1, 2017 8:25 PM, Mishelle Oña
wrote:
Hello everybody,
I have a question about t
Hi,
So, you want to make a selection according to a geometric criterion, which
is what gmx select does.
Mark
On Mon, Apr 3, 2017 at 10:12 AM ISHRAT JAHAN wrote:
> i want to calculate number of water molecule within given distance from
> protein.
>
>
> On Mon, Apr 3, 2017 at 1:20 PM, Mark Abrah
I think you should set it for what you consider as solvent.
On Saturday, April 1, 2017 8:39 PM, Pranesh M
wrote:
Dear All,
I am trying to generate simulation for ionic liquid and aromatic compound.
No water molecule is involved in my system.
In the NPT.mdp file parameters, should I ch
i want to calculate number of water molecule within given distance from
protein.
On Mon, Apr 3, 2017 at 1:20 PM, Mark Abraham
wrote:
> Hi,
>
> It's not clear to me what you actually want, or why trjorder is even a
> possible tool for the job. Look at
> http://manual.gromacs.org/documentation/20
Hi,
It's not clear to me what you actually want, or why trjorder is even a
possible tool for the job. Look at
http://manual.gromacs.org/documentation/2016/user-guide/cmdline.html and
find something useful.
Mark
On Mon, Apr 3, 2017 at 9:46 AM ISHRAT JAHAN wrote:
> -- Forwarded message -
-- Forwarded message --
From: ISHRAT JAHAN
Date: Fri, Mar 31, 2017 at 12:51 PM
Subject: analysis of osmolyte at particular distance from backbone
To: gmx-us...@gromacs.org
Dear all,
I want to calculate the number of osmolyte molecule at particular distance
from backbone with res
Hi,
I imagine it does whatever is standard, e.g. from negative to positive.
What does it report for a single water molecule?
Mark
On Mon, Apr 3, 2017 at 8:24 AM Alex wrote:
> No comment on below question, please?
>
> Regards,
> Alex
>
> -- Forwarded message --
> From: Alex
> D
Hi,
See
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume
Mark
On Mon, Apr 3, 2017 at 9:27 AM Aman Deep wrote:
> sir is there any way to create only XTC file from mdrun only. the server on
> which I am working is not providing enough space and my trr file is too
>
sir is there any way to create only XTC file from mdrun only. the server on
which I am working is not providing enough space and my trr file is too
much large.
thank you
--
Aman Deep
MSc Bioinformatics
Jamia Millia Islamia
New Delhi - 110025
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