Thank you Dr. Dallas. Yes I think the issue is that the starting
conformation is linear, as I want to study its folding properties. I tried
the same with helical starting conformation, and got around 11 water
molecules, which is still ok.
I am trying to find a way to simulate a 89 aa peptide in
>From the box volume printed in the script output it appears you have a box
>that is approximately a 28nm cube. And that size box requires a significant
>number of water molecules to fill up, so that number you have in there
>(~770,000) seems about correct.
If you want to have less water molec
Dear all,
I am trying to see the folding of a 89 aa peptide. So I am setting up the
system from linear conformation.
I gave the following commands to build the box and add the solvent
molecules.
editconf -f output.gro -c -d 1.0 -bt dodecahedron -o outbox.gro
genbox -cp outbox.gro -cs spc216.gro
Dear Sir,
Here's the result for the REMD trial with large temperature gaps.
Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4
447.1 471.0 496.1 522.6 550.5 579.9 610.8
Out of md16.log :
Replica exchange statistics
Repl 249 attempts, 125 odd, 124 even
Repl average prob
On 5/13/13 8:23 PM, Marcelo Vanean wrote:
Hi. I'm with doubts concerning the charge groups. I am simulating ethylene
glycol and the only way of charged groups are neutral is putting all atoms
in only one charge group. This is advisable? Is that a problem? What is the
greatest number of atoms in
Hi. I'm with doubts concerning the charge groups. I am simulating ethylene
glycol and the only way of charged groups are neutral is putting all atoms
in only one charge group. This is advisable? Is that a problem? What is the
greatest number of atoms in a charge group which is recommended?
--
gmx-
That really depends on where the function that you are using comes from and
what forcefield you are using (because each forcefield can treat them
differently). If it is the one for alkane chains mentioned in the manual to be
used with the GROMOS FFs, then as it states in the manual you have to
On 5/13/13 6:24 PM, Marcelo Vanean wrote:
Hello to all. I am simulating long-chain alcohols. For the dihedrals, I
used Rycaert-Bellemans function. In this case I should delete the pairs
from topology?
That depends on which force field you are using. See manual section 4.2.12.
-Justin
--
=
Hello to all. I am simulating long-chain alcohols. For the dihedrals, I
used Rycaert-Bellemans function. In this case I should delete the pairs
from topology?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http
On 5/13/13 11:50 AM, Laura Leay wrote:
All,
I've seen a few threads about simulations in ionic liquds but have not come
across anything that tells me what settings I should use in my mdp file. The
system is nitric acid which has fully dissociated into NO3- and HO3+. The
simulation will run
Hi,
I'm new to Gromacs. How to convert NMR paramagnetic relaxation enhancement
distance restraints into gromacs format in topol.top file for structural MD
refinement.
--Rama
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Distance-Restraints-tp5008207.html
Sent from the GR
Here is the script:
#!/bin/bash
# note: you must have "par_all27_prot_lipid.prm" in the starting directory
set -e
PROGRAMS="/g1/home/resal/Programs"
GMX_BIN_457="$PROGRAMS/gromacs/4.5.7/thread/bin"
GMX_BIN_461="$PROGRAMS/gromacs/4.6.1/thread/bin"
NMD_BIN="$PROGRAMS/namd/NAMD_2.9_Linux-x86_64-mu
So I think I figured out what was causing the discrepancy of Charmm27 energies
between gromacs and NAMD. It appears that it's related to the gromacs version:
energies from 4.5.7 and NAMD match very well while 4.6.1 gives energies that
are different from both 4.5.7 and NAMD.
Here are the results
As usual there is no universal question, it depends on what do you want
to see from your MD.
The main factor to consider is the disk space that you can use if
you decide to save every 10 ps it means that for 100ns you'll have
10.000 frame, depending on your system this can be a huge amount of
d
Hi,
the manual mentions that with the option '-surf' no normalization is
done. So it's normal the RDF will inrease with larger distances, since
the further you'll go away from the protein, the bigger the spherical
shell is (from which the RDF for distance r is calculated) and the more
water mo
All,
I've seen a few threads about simulations in ionic liquds but have not come
across anything that tells me what settings I should use in my mdp file. The
system is nitric acid which has fully dissociated into NO3- and HO3+. The
simulation will run fine with just the ions at low density unde
You need to increase the temperature gaps indeed if you want acceptance ratio
~0.2/0.3. But again this won't work with the water …
It is not clear what happens in your index file but probably a problem from
grace to plot so many points … you can try to increase the "Max drawing path
length" i
Dear Sir,
I repeated the simulation again for 25 replicas with the following temp.
distribution .
280
289.1
298.5
308.2
318.2
328.6
339.3
350.3
361.7
373.5
385.6
398.1
411.1
424.4
438.3
452.5
467.2
482.4
498.1
514.3
531.0
548.3
566.1
584.5
603.5
623.2
The output of md.log file is :-
Replica exc
On 5/13/13 9:51 AM, DavidPO wrote:
Dear GROMACS support!
For my experiment I should use QM/MM methods. For this reason I should link
mdrun program with ORCA.
I'm working with 4.6 gromacs version and doing following:
download ORCA on my computer;
set the flags:
BASENAME
Dear Gmx Users,
I run long simulation of my protein with 50 small molecules in water.
I calculated the RDF (Protein - Water) using -surf mol and -rdf mol_com.
Please, take a look at my plot:
http://speedy.sh/tmJbD/rdf-P-W.png
Could you please, explain me why the second peak is so high? Shall I u
Dear GROMACS support!
For my experiment I should use QM/MM methods. For this reason I should link
mdrun program with ORCA.
I'm working with 4.6 gromacs version and doing following:
download ORCA on my computer;
set the flags:
BASENAME=topol
ORCA_PATH=/home/timofeev/
On 5/13/13 9:45 AM, Brighter Agyemang wrote:
Please thanks so much for your support but I still do not get what all you
are talking about is
These posts are not related to your question. Reading posts on other topics can
be very informative and should be augmented by literature and tex
Please thanks so much for your support but I still do not get what all you
are talking about is
On 13 May 2013 11:44, Justin Lemkul wrote:
>
>
> On 5/13/13 1:48 AM, Acoot Brett wrote:
>
>> Dear All,
>>
>> Will you please explain how the initial velocity may affect the MD
>> results?
>>
>
>
Ok, the redmine is filled up and anybody who has time to help finding the issue
is welcome :) I can't do much more!
As an alternative a colleague suggested that I could potentially get around the
problem by using a compilation combining Open-MP or thread-MPI for each replica
running on one nod
Thanks a lot for your answer.
So by increasing the z coordinate after solvated the system we induce
creation of a empty space above the solvated box.
After minimisation a few water molecules move above its new empty space
because their link are not strong enough.
2013/5/13 Justin Lemkul
>
>
> O
thank you for the reply, I'm in contact with my admin and I hope that he
will tell me something soon.
One thing that I really don't understand is why only the last
nanoseconds are "affected".
I run the same simulation (with the same paramenters) and I've never had
problems in the first 4 ns , only
On 5/13/13 8:01 AM, Nawel Mele wrote:
So we just compute an interface vacuum-water like the picture in attach in
increase the coordinate value of the z-axis of the box?
The list does not accept attachments. If you want to post an image or file,
provide a public link to access it.
BUt I d
Dear All,
I am running a simulation of ligand binding in a protein. Ligand is
mostly negatively charged, so as expected it should bind to the positive
region of the protein. To check the possible binding zone, I try to
calculate or rather visualize the electrostatic potential map of a protein
So we just compute an interface vacuum-water like the picture in attach in
increase the coordinate value of the z-axis of the box?
BUt I don't understand how just like that we creat an empty place and water
move to this place??
2013/5/13 Justin Lemkul
>
>
> On 5/13/13 6:10 AM, Nawel Mele wrote
- Forwarded Message -
From: Justin Lemkul
To: mohammad agha
Cc:
Sent: Monday, May 13, 2013 4:11 PM
Subject: Re: probability from COM of micelle
It is much better to post this information to the list so that others can
benefit from it.
-Justin
On 5/13/13 5:25 AM, mohammad agha wr
On 5/13/13 6:41 AM, Francesco wrote:
Good morning all,
This morning I checked the output of a 8ns (4 x 2ns) of simulation and I
noticed a strange behaviour:
The fist two simulations (each 2ns) ended up correctly and they both
took 2h 06min to finish.
The second two were still running when the c
On 5/13/13 6:30 AM, Laura Leay wrote:
All, I have a system of nitric acid modelled as NO3- and HO3+ plus SPC water.
After setting the system up using genbox I then energy minimise. Althouth the
input conf.gro file looks fine (NO3- labelled 'NO3', HO3+ labelled 'HO3' and
water labelled 'SOL')
On 5/13/13 6:10 AM, Nawel Mele wrote:
Hi all,
I am performing a simulation of protein at air/water interface.
For create an air-water interface I just expand the box in the z direction.
So,aAfter minimization we can noticed that water molecules moved out of
bulk water in the z direction.
Why
On 5/13/13 5:33 AM, Arunima Shilpi wrote:
Respected Sir
many many thanks for your reply to my last mail. I was able able to debug
the error
Here I have new set of queries..
How much COM spacing should i consider for my protein-ligand interactiom
How much total distance I should move along z-a
On 5/13/13 4:44 AM, Sainitin Donakonda wrote:
Thank you very much for inputs but i forgot to mention in previous query i
got one error ..with other protein ligand simulation i used same MD file
saving 200 steps..
*Cannot write trajectory frame; maybe you are out of quota?*
*
*
Whats the soluti
On 5/13/13 1:48 AM, Acoot Brett wrote:
Dear All,
Will you please explain how the initial velocity may affect the MD results?
We use different initial velocities to improve sampling, i.e. to allow the
trajectory to evolve in different ways. In the end, in the limit of infinite
sampling, th
Hi,
it seems that you've only coupled your protein to the thermostat, but
not the solvent, hence the error message.
Generally one would couple both domains of the protein to one thermostat
and the solvent (inluding ions) to another thermostat.
Side note: If you want to use the WHAM method for
Good morning all,
This morning I checked the output of a 8ns (4 x 2ns) of simulation and I
noticed a strange behaviour:
The fist two simulations (each 2ns) ended up correctly and they both
took 2h 06min to finish.
The second two were still running when the cluster time was over (I
asked for 2.30)
Dear,
i want to study how ligands change the conformations using the gromacs
software and i want to run 100ns, but i don't konw how to reasonably set the
nstxout nstvout nstenergy nstlog and nstxtcout.
Thank you very much!
--
gmx-users mailing listgmx-users@gromacs.org
http:/
All, I have a system of nitric acid modelled as NO3- and HO3+ plus SPC water.
After setting the system up using genbox I then energy minimise. Althouth the
input conf.gro file looks fine (NO3- labelled 'NO3', HO3+ labelled 'HO3' and
water labelled 'SOL') the confout file has all of the H3O renam
Hi all,
I am performing a simulation of protein at air/water interface.
For create an air-water interface I just expand the box in the z direction.
So,aAfter minimization we can noticed that water molecules moved out of
bulk water in the z direction.
Why you just need to expand the z-axis for ob
Respected Sir
many many thanks for your reply to my last mail. I was able able to debug
the error
Here I have new set of queries..
How much COM spacing should i consider for my protein-ligand interactiom
How much total distance I should move along z-axis/...
and which all conf file should i take
Thank you very much for inputs but i forgot to mention in previous query i
got one error ..with other protein ligand simulation i used same MD file
saving 200 steps..
*Cannot write trajectory frame; maybe you are out of quota?*
*
*
Whats the solution for this error ? is this same problem with savi
Thanks a lot for your answer.
2013/5/10 Justin Lemkul
>
>
> On 5/10/13 4:24 AM, Nawel Mele wrote:
>
>> Hi,
>>
>> I am trying to understand what is the difference between g_rms and
>> g_rmsdist commands.
>> I have looked at the manual and all I can find is that:
>>
>> *g_rms*: The root mean squar
HI,
I would like to compute an umbrella sampling simulation for o protein
divided in two domain, with Center of mass pulling using as constraint
between the two domains. And the constraint is applied instead of a
harmonic potential
I create a pull.mdp file with this option for the pull:
title
On 13/05/2013 08:46, "Sainitin Donakonda" wrote:
>Hello,
>
>I am trying to run 20 ns protein ligand simulation on cluster using
>following MD.MDP file
>
>; 7.3.3 Run Control
>integrator = md; leap-frog integrator
>dt = 0.002
You may have created large files and thus got out of quota on the disc.
Check your quota and consider reducing the frequency of saving coordinates.
On May 13, 2013, at 9:46, Sainitin Donakonda wrote:
> Hello,
>
> I am trying to run 20 ns protein ligand simulation on cluster using
> followin
Hello,
I am trying to run 20 ns protein ligand simulation on cluster using
following MD.MDP file
; 7.3.3 Run Control
integrator = md; leap-frog integrator
dt = 0.002 ; 2 fs
nsteps = 500; max
Huyjin,
If you look in your log file from the rerun you will see that when running
using the GPU, energy groups are ignored or unused for energy reporting. Thus
for this to work you need to run it on the CPUs.
This is what I get in my output md.log when trying the same thing...
>> NOTE: With GP
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