By "crash" I meant "explode" not "DD is impossible." Explosions don't
happen because of parallelism, they happen because the steps are too large
for the size of the forces. The forces required to stably expand a box from
20A to 70A seem likely to be so large that I am very skeptical that you
could
If the job is not "very parallel", it will not crash.
It is better to preequilibrate in NVT beforehand. Cyclopropylchloride
is probably a liquid at 290K, if the model is parametrized reasonably.
So it should not phase-separate.
Vitaly
On Wed, Oct 23, 2013 at 11:29 AM, Mark Abraham wrote:
> On
On Oct 23, 2013 5:34 AM, "Nilesh Dhumal" wrote:
>
> Hello,
>
> I am running a NPT simulation for cyclopropylchloride(1) in
> 50%water(100)+50%ethanol(100) using opls force field parameter .
>
> After equilibration box size increases from 20 A to 70 A.
Really? Seems wildly unlikely to have occurre
Hello,
I am running a NPT simulation for cyclopropylchloride(1) in
50%water(100)+50%ethanol(100) using opls force field parameter .
After equilibration box size increases from 20 A to 70 A.
I used the following mdp file.
; RUN CONTROL PARAMETERS =
integrator = sd
; start time and
Previous message: [gmx-users] Box size/type confusion for bilayer system
Next message: [gmx-users] Box size/type confusion for bilayer system
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
On 10/18/12 2:43 PM, klexa wrote:
> Hi Gromacs users,
>
> I think I am a bit confused
On 2012-10-18 03:58:22PM -0400, Justin Lemkul wrote:
>
>
> On 10/18/12 3:55 PM, Peter C. Lai wrote:
> > On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote:
> >>
> >>
> >> On 10/18/12 2:43 PM, klexa wrote:
> >>> Hi Gromacs users,
> >>>
> >>> I think I am a bit confused about the proper way to han
On 10/18/12 3:55 PM, Peter C. Lai wrote:
On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote:
On 10/18/12 2:43 PM, klexa wrote:
Hi Gromacs users,
I think I am a bit confused about the proper way to handle boxes that are not
standard cubes. I'm trying to run a membrane simulation where a cy
On 2012-10-18 02:53:38PM -0400, Justin Lemkul wrote:
>
>
> On 10/18/12 2:43 PM, klexa wrote:
> > Hi Gromacs users,
> >
> > I think I am a bit confused about the proper way to handle boxes that are
> > not
> > standard cubes. I'm trying to run a membrane simulation where a cyclic
> > undecapeptid
On 10/18/12 3:04 PM, klexa wrote:
On 10/18/2012 11:53 AM, Justin Lemkul wrote:
On 10/18/12 2:43 PM, klexa wrote:
Hi Gromacs users,
I think I am a bit confused about the proper way to handle boxes that are not
standard cubes. I'm trying to run a membrane simulation where a cyclic
undecapept
On 10/18/2012 11:53 AM, Justin Lemkul wrote:
On 10/18/12 2:43 PM, klexa wrote:
Hi Gromacs users,
I think I am a bit confused about the proper way to handle boxes
that are not
standard cubes. I'm trying to run a membrane simulation where a cyclic
undecapeptide is inserted into the membrane
On 10/18/12 2:43 PM, klexa wrote:
Hi Gromacs users,
I think I am a bit confused about the proper way to handle boxes that are not
standard cubes. I'm trying to run a membrane simulation where a cyclic
undecapeptide is inserted into the membrane and I want the water layer to be
sufficiently thi
Hi Gromacs users,
I think I am a bit confused about the proper way to handle boxes that
are not standard cubes. I'm trying to run a membrane simulation where
a cyclic undecapeptide is inserted into the membrane and I want the
water layer to be sufficiently thick that if it were pulled, the
Mark
Greetings
Lara
*Von:* Justin A. Lemkul
*An:* Lara Bunte ; Discussion list for GROMACS
users
*Gesendet:* 17:28 Donnerstag, 22.März 2012
*Betreff:* Re: [gmx-users] Box Size in MD
Lara Bunte wrote:
> Hello
>
for GROMACS users
Gesendet: 17:28 Donnerstag, 22.März 2012
Betreff: Re: [gmx-users] Box Size in MD
Lara Bunte wrote:
> Hello
>
> What size should a box have in that you do your MD? I always read that for
> short Lennard Jones interactions one should do a cut off with the half
Lara Bunte wrote:
Hello
What size should a box have in that you do your MD? I always read that for
short Lennard Jones interactions one should do a cut off with the half of the
box size but what how to know a good box size?
This is not correct. The cutoffs are dictated by the force field y
Hi Lara,
The cut-offs are pretty much part of the force field. One rule is that
the distance between periodic images should be larger than the cutoff.
For protein/solute simulations that translates in a minimal distance
between the solute and the wall of half the cutoff used. Another rule
is based
As far as I concern, the minimum size is that cove all parts of your
molecules or system. In case you should use solvent it is up to you to add
how many molecules and in this case you should make decision by experience
or according to literature.
Dariush
--
Kind Regards,
Dariush Mohammadyani
D
Hello
What size should a box have in that you do your MD? I always read that for
short Lennard Jones interactions one should do a cut off with the half of the
box size but what how to know a good box size?
Thanks for help
Greetings
Lara
--
gmx-users mailing listgmx-users@gromacs.org
http://
On 17/08/2011 9:13 PM, Kavyashree M wrote:
Sir,
I checked gmxdump -e ener.edr as suggested, I found that
there are exactly 10001 values for Box-X/Y/Z with 7.,7 and 5
when I calculated the average for these values using another
tool I got 7.2, 7.2 and 5.1 as expected. But g_energy gave
some diffe
Sir,
I checked gmxdump -e ener.edr as suggested, I found that
there are exactly 10001 values for Box-X/Y/Z with 7.,7 and 5
when I calculated the average for these values using another
tool I got 7.2, 7.2 and 5.1 as expected. But g_energy gave
some different answer as mentioned before in both 4.5.3
Sorry Sir,
I did not get that mail from the forum.
Thank you
With Regards
Kavya
On Wed, Aug 17, 2011 at 12:11 PM, Tsjerk Wassenaar wrote:
> This mail was answered already... Please pay attention.
>
> http://lists.gromacs.org/pipermail/gmx-users/2011-August/063814.html
>
> Tsjerk
>
> On Wed, Aug
This mail was answered already... Please pay attention.
http://lists.gromacs.org/pipermail/gmx-users/2011-August/063814.html
Tsjerk
On Wed, Aug 17, 2011 at 8:12 AM, Kavyashree M wrote:
> Dear users,
>
> While calculating the box dimensions during a simulation
> of 20ns I got some strange values
Dear users,
While calculating the box dimensions during a simulation
of 20ns I got some strange values of the averages -
Command used:
g_energy -f ener.edr -o box.xvg
Output:
Energy Average Err.Est. RMSD Tot-Drift
On 16/08/11, Kavyashree M wrote:
>
> Dear users,
>
> While calculating the box dimensions during a simulation
> of 20ns I got some strange values of the averages -
>
> Command used:
> g_energy -f ener.edr -o box.xvg
>
> Output:
> Energy Average Err.Est. RMSD
Dear users,
While calculating the box dimensions during a simulation
of 20ns I got some strange values of the averages -
Command used:
g_energy -f ener.edr -o box.xvg
Output:
Energy Average Err.Est. RMSD Tot-Drift
Andrew DeYoung wrote:
Hi,
I have tried to run a simulation of 1000 SPC/E water molecules. I have a
PDB file containing a 10 by 10 by 10 regular array (cube) of water
molecules, each separated by approximately 6 Angstroms. I used pdb2gmx to
convert the PDB file to GRO and topology, selecting
Hi,
I have tried to run a simulation of 1000 SPC/E water molecules. I have a
PDB file containing a 10 by 10 by 10 regular array (cube) of water
molecules, each separated by approximately 6 Angstroms. I used pdb2gmx to
convert the PDB file to GRO and topology, selecting the OPLS-AA force field
an
On 1/23/11 12:58 PM, Christian Mötzing wrote:
Am Sonntag, den 23.01.2011, 09:40 +1100 schrieb Mark Abraham:
On 23/01/2011 2:36 AM, Christian Mötzing wrote:
Am Samstag, den 22.01.2011, 11:39 +1100 schrieb Mark Abraham:
On 21/01/2011 6:47 AM, Christian Mötzing wrote:
Hi,
I currently read thr
Am Sonntag, den 23.01.2011, 09:40 +1100 schrieb Mark Abraham:
> On 23/01/2011 2:36 AM, Christian Mötzing wrote:
> > Am Samstag, den 22.01.2011, 11:39 +1100 schrieb Mark Abraham:
> >> On 21/01/2011 6:47 AM, Christian Mötzing wrote:
> >>> Hi,
> >>>
> >>> I currently read through the GMX manual 4.5.3
On 23/01/2011 2:36 AM, Christian Mötzing wrote:
Am Samstag, den 22.01.2011, 11:39 +1100 schrieb Mark Abraham:
On 21/01/2011 6:47 AM, Christian Mötzing wrote:
Hi,
I currently read through the GMX manual 4.5.3. I have two questions:
1) Density is calculated by the density of the material and th
Am Samstag, den 22.01.2011, 11:39 +1100 schrieb Mark Abraham:
> On 21/01/2011 6:47 AM, Christian Mötzing wrote:
> > Hi,
> >
> > I currently read through the GMX manual 4.5.3. I have two questions:
> >
> > 1) Density is calculated by the density of the material and the box
> > volume. But I can't f
On 21/01/2011 6:47 AM, Christian Mötzing wrote:
Hi,
I currently read through the GMX manual 4.5.3. I have two questions:
1) Density is calculated by the density of the material and the box
volume. But I can't find a reference on how the box size is calculated.
Can you point me to some literatur
Hi,
I currently read through the GMX manual 4.5.3. I have two questions:
1) Density is calculated by the density of the material and the box
volume. But I can't find a reference on how the box size is calculated.
Can you point me to some literature?
2) I wanted to look up the calculation of the
On Fri, Dec 24, 2010 at 8:12 AM, Amit Choubey wrote:
>
>
> On Thu, Dec 23, 2010 at 2:41 PM, mustafa bilsel wrote:
>
>> Hi,
>>
>> 1. How can I learn the box shape and size of a completed simulation?
>>
>
> check the end of the resulting gro file .
>
>
>> 2. I want to keep going the previous comple
On Thu, Dec 23, 2010 at 2:41 PM, mustafa bilsel wrote:
> Hi,
>
> 1. How can I learn the box shape and size of a completed simulation?
>
check the end of the resulting gro file .
> 2. I want to keep going the previous completed energy minimization by
> increasing nsteps. How can I do this?
>
i
Hi,
1. How can I learn the box shape and size of a completed simulation?
2. I want to keep going the previous completed energy minimization by
increasing nsteps. How can I do this?
Best wishes
Mustafa
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gm
noob noob wrote:
Dear all,
I am new about MD simulation and I have some questions about the box
size.
I had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5
nm ) but now I change to a bigger molecules and increase the number of
molecules. So,the new system cannot fix into t
Dear all,
I am new about MD simulation and I have some questions about the box size.
I
had performed 1 simulation previously ( box size of 5 nm x 5 nm x 5 nm
) but now I change to a bigger molecules and increase the number of
molecules. So,the new system cannot fix into the previous box.
There
Hi,
On Friday, 31. October 2008, Andrea Muntean wrote:
> Hi all,
>
> I have my box defined at the end of my pdb file as (lenghts in Angstrom)
>
> AXAYAZt 70.70. 112.0777 5800.
In the pdb file the box information is normally defined in the beginning of
the file with
CRYS
Hi all,
I have my box defined at the end of my pdb file as (lenghts in Angstrom)
AXAYAZt 70.70. 112.0777 5800.
In the gro file (produced by pdb2gmx) I get
2.51900 2.84400 6.80610
on the last line. Is this my box reduced to the size of the molecule?
Or what does
ce it has been fixed for
4.0.
Berk.
> Date: Thu, 24 Jul 2008 14:55:24 -0400
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] box size changing during isotropic pressure coupling
>
> >Here tau_p=4, which is already quite large.
> >But there are
Here tau_p=4, which is already quite large.
But there are no "real" problems in the system, the results should be fine.
But the relative ling tau_p might be the reason for the strange scaling.
This would make the scaling factor always close to 1 plus or minus one bit.
I have not done the binary ma
Thanks for the assistance Berk,
Hmm... this is a (seemingly( really systematic decrease in x and y and increase
in z.
But is x at the start really EXACTLY identical to y?
No. Here are the starting dimensions:
19.58000 19.39000 21.04200
That is prior to 200ps run with position restraints
t done the binary math, so I can not see if somehow this would
make numbers slightly below 20 scale down and above 20 scale up.
Berk.
> Date: Thu, 24 Jul 2008 13:40:02 +0200
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] box size changing during isotr
doesn't seem to
exist anymore.
Berk.
> Date: Fri, 18 Jul 2008 13:54:19 -0400
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] box size changing during isotropic pressure coupling
>
> Hello,
>
> I have a system of 750,000 atoms con
y are treated differently (although adding only zeros),
so depending on the compiler, the results could differ by a bit.
What system and compiler are you using?
Berk.
> Date: Fri, 18 Jul 2008 13:54:19 -0400
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-use
Hello,
I have a system of 750,000 atoms consisting of detergent in water.
Although this run has been carried out using isotropic pressure
coupling, I see significant drift in the box dimensions over 150 ns.
This run was carried out using gromacs version 3.3 and 3.3.1. I used the
-shuffle and
A knowledgeable and helpful gromacs user has pointed me to some
bugzilla comments: http://bugzilla.gromacs.org/show_bug.cgi?id=165
that reference revision comments:
http://www.gromacs.org/gromacs/revisions/
Berk Hess
13 Feb 2008
box distortion with pressure coupling
In all Gromacs versions
Hi,
Read a bit more carefully though. A cubic box is based on the
circumscribed sphere of the solute, dilated with the desired distance
between the solute and the wall (and it has nothing to do with
calculation of the solvation surface, which to me sounds to be related
to solvent accessible surfac
Chih-Ying Lin wrote:
Hi
1. in the last row of .gro file, the three number represent the length
of the box on X, Y , and Z directions in nanometer.
Right??
These values represents the real dimensions of the box
2. for the editconf command,
editconf -d Distance_between_the_solute_and_the
Chih-Ying Lin wrote:
Hi
1. in the last row of .gro file, the three number represent the length
of the box on X, Y , and Z directions in nanometer.
Right??
These values represents the real dimensions of the box
2. for the editconf command,
editconf -d Distance_between_the_solute_and_the
Hi
1. in the last row of .gro file, the three number represent the length
of the box on X, Y , and Z directions in nanometer.
Right??
2. for the editconf command,
editconf -d Distance_between_the_solute_and_the_box bt cubic
Right??
what are the differences between the three number in th
Arnab Senapati wrote:
Hello,
I was trying to run a simple LJ system. In the conf.gro box size is
7.52 (cubic). But in the confout.gro the box size is 9.1. Is this
possible?
Yes, since it happened. :-) If you're trying to understand what it is
that you've done that has caused the change,
Hello,
I was trying to run a simple LJ system. In the conf.gro box size is
7.52 (cubic). But in the confout.gro the box size is 9.1. Is this
possible?
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
__
t; and a warning in the log file as
> " the box size exploding".
>
> Very grateful for your advice and help!!!
>
> Nancy
>
>
>
>
> - Original Message - From: "Mark Abraham"
> <[EMAIL PROTECTED]>
> To: "Discussion list for GROMACS use
a warning in the log file as
" the box size exploding".
Very grateful for your advice and help!!!
Nancy
- Original Message - From: "Mark Abraham"
<[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users"
Sent: Wednesday, February 28, 2007 5:1
ot;.
Very grateful for your advice and help!!!
Nancy
- Original Message -
From: "Mark Abraham" <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users"
Sent: Wednesday, February 28, 2007 5:15 PM
Subject: Re: [gmx-users] box size changed
Nancy Deng w
Nancy,
My guess is that you have pressure coupling on. Now, what is the
characteristic of vacuum? What will happen if you have a balloon
filled with vacuum (and one small red car of almost negligible size)
and you couple it to a reference pressure (keep it out in the
air)?
In the other case,
Nancy Deng wrote:
Hi Mark,
Thanks for the quick response and the funny story :)
I indeed want to collect the possible comformation of a certain small
molecule (a little car made of 35 atoms around 15 A in length) by MD.
Since obvious to my understanding that in vacume or in water
environment
age -
From: "Mark Abraham" <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users"
Sent: Wednesday, February 28, 2007 3:42 PM
Subject: Re: [gmx-users] box size changed
Nancy Deng wrote:
Dear All,
I am a very beginner of Gromacs and currently trying to run t
Nancy Deng wrote:
Dear All,
I am a very beginner of Gromacs and currently trying to run two small
molecule (35 atoms) MD studies, one with water and the other without
water (skip the "genbox" step).
Surprisingly, the box size of the system containing only small molecule
(without water) kept
Dear All,
I am a very beginner of Gromacs and currently trying to run two small
molecule (35 atoms) MD studies, one with water and the other without water
(skip the "genbox" step).
Surprisingly, the box size of the system containing only small molecule
(without water) kept shrink till the pr
Original Message
From: Mohamed Osman <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Thursday, January 11, 2007 10:49:29 PM
Subject: [gmx-users] box size for simulation of membrane protein
My questions:
1. Protein is closer to one edge than the other. Does this ma
I am going to start by quoting: Chapter 3 of the Gromacs manual (page 14)
"length of each box vector must exceed the length of the macromolecule in
the direction of that edge plus two times the cutoff radius Rc"Then it
states:
"It is common to compormize in this respect and make the solvant
64 matches
Mail list logo
