Hi,
I tried to run on single node now. Now the error is different saying
"One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off"
This means that my box shrinks during dynamics (this is not constant volume MD)
But
nikhil damle wrote:
Hi,
I tried to run on single node now. Now the error is different saying
"One of the box vectors has become shorter than twice the cut-off length
or box_yy-|box_zy| or box_zz has become smaller than the cut-off"
This means that my box shrinks during dynamics (this is not c
Berk Hess wrote:
> Date: Wed, 7 Oct 2009 15:51:00 +0200
> From: joc...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] vsites and lincs-order
>
> All right, thanks!
>
> Since you mention energy conservation, maybe it would be worth adding
> notes or a warnings into pdb2gmx
No. My system is a single protein with charged ligand associated with it. But
why should box size shrink ? In solvated system it does not shrink. What effect
vacuum could possibly have on it ?
Regards,
Nikhil
From: Mark Abraham
To: Discussion list for GROMAC
Hi,
I used gmxcheck and gxmdump to compare the results of two simulations on an
identical system but using two different tabulated potential, one harmonic (the
simulation ended correctly) and one not. There are no differences in terms of
non bonded interactions, other energy terms and the param
Hi,
The required spacing is basically only related with the second derivative of
the potential
and the accuracy you want. In "standard" cases, your spacing of 0.001 nm should
be enough.
But if your potential comes from some numerical inversion procedure, your
potential could
be very noisy, whi
Now when i increased the fourierspacing from 0.12 to 0.22 nm, it worked
properly on single node and failed on multiple nodes giving same error of
"The Y-size of the box (4.612312) times the triclinic skew factor (0.866052) is
smaller than the number of DD cells (2) times the smallest allowed cell
Hi,
Do not "randomly" change the fourierspacing.
Are you really using PME in vacuum?
The box size can only change if you have pressure coupling turned on,
which should, obviously, should not do in vacuum.
Berk
Date: Thu, 8 Oct 2009 15:13:25 +0530
From: pdnik...@yahoo.co.in
Subject: Re: [gmx-us
Smith, Chanel Chonda wrote:
In the drug-enzyme tutorial it says that the crude was refined using a
certain force field, SD, and CG. How was this accomplished?
Then parameters from that force field (like charges and charge groups from
analogous functional groups) were probably assigned, foll
Hi,
sorry for answering late, I was on vacation. If you have not tried it
already,
I would say that a direct back-to-back connection will give you a few
percent
extra in scaling, but probably not more. The sad thing about Ethernet
is that
its throughput is fixed while the performance of the
Rossen Apostolov ha scritto:
> Hi,
>
> I made some updates and incorrectly changed the permissions.
> You should be able to search now even without logging in.
>
I jump in this thread to ask: I've notice that there are a huge amount
of broken links in the new Gromacs pages. This is bad for me si
ms wrote:
Rossen Apostolov ha scritto:
Hi,
I made some updates and incorrectly changed the permissions.
You should be able to search now even without logging in.
I jump in this thread to ask: I've notice that there are a huge amount
of broken links in the new Gromacs pages. This is bad for
Justin A. Lemkul ha scritto:
>
>
> ms wrote:
>> Rossen Apostolov ha scritto:
>>> Hi,
>>>
>>> I made some updates and incorrectly changed the permissions.
>>> You should be able to search now even without logging in.
>>>
>>
>> I jump in this thread to ask: I've notice that there are a huge amount
ms wrote:
Justin A. Lemkul ha scritto:
ms wrote:
Rossen Apostolov ha scritto:
Hi,
I made some updates and incorrectly changed the permissions.
You should be able to search now even without logging in.
I jump in this thread to ask: I've notice that there are a huge amount
of broken links
Justin A. Lemkul ha scritto:
Google cache and the PDF manual are my friends, but any hint on
where to
retrieve the pages that are still linked as being on the old wiki is
appreciated.
>>> The old wiki has been taken down. You can search the Gromacs site (not
>>> the mailin
ms wrote:
Justin A. Lemkul ha scritto:
Google cache and the PDF manual are my friends, but any hint on
where to
retrieve the pages that are still linked as being on the old wiki is
appreciated.
The old wiki has been taken down. You can search the Gromacs site (not
the mailing list) for rele
Justin A. Lemkul ha scritto:
> ms wrote:
>> Justin A. Lemkul ha scritto:
>> Google cache and the PDF manual are my friends, but any hint on
>> where to
>> retrieve the pages that are still linked as being on the old wiki is
>> appreciated.
>>
> The old wiki has been taken do
Berk Hess wrote:
Hi,
Do not "randomly" change the fourierspacing.
Are you really using PME in vacuum?
The box size can only change if you have pressure coupling turned on,
which should, obviously, should not do in vacuum.
This suggests adding a warning about pressure coupling when the atomic
ms wrote:
Justin A. Lemkul ha scritto:
ms wrote:
Justin A. Lemkul ha scritto:
Google cache and the PDF manual are my friends, but any hint on
where to
retrieve the pages that are still linked as being on the old wiki is
appreciated.
The old wiki has been taken down. You can search the Gro
Mark Abraham escreveu:
Alexandre Suman de Araujo wrote:
Hi Gmxers
Some months ago I performed some simulations, with GMX 3.3.3 version,
where I apply distance restraint between water oxygen atoms and a
static dummy site located at the center of a sphere to keep waters
inside this sphere. Aft
Justin A. Lemkul ha scritto:
>>> The old wiki has been taken down. You can search the Gromacs site
>>> (not
>>> the mailing list) for relevant content, until all the links are
>>> working. There has been some discussion about this lately; it will
>>> be a
>>> very time-con
ms wrote:
Justin A. Lemkul ha scritto:
The old wiki has been taken down. You can search the Gromacs site
(not
the mailing list) for relevant content, until all the links are
working. There has been some discussion about this lately; it will
be a
very time-consuming task.
Searching I tried,
Hi Berk,
the potential I used comes indeed from Boltzmann inversion but I fitted it with
a polynomial function of suitable degree which gave an almost perfect agreement
on the range chosen (outside this range it reproduces the correct repulsive
branches of the potential). I generated the tabula
Justin A. Lemkul ha scritto:
>> Well, I'd like to help with fixing the links whenever I find a broken
>> one, but it seems I can't edit. :)
>>
> You have to register as a contributer and log in (top right of the
> Gromacs page).
I registered yesterday and I am logged in, b
Hi,
I am very hesitant to put in such checks.
In most cases they would not be necessary.
I a few cases it would help a user that does not know exactly would he/she is
doing.
But I don't like to make life harder for people who do know what they are doing
and are simulating systems that are not th
Hi all,
I am trying to simulate 100 molecules of n-alkane molecules but keep
receiving LINC errors.
When I completed steepest descent I received following msg:
Steepest Descents converged to Fmax < 500 in 819 steps
Potential Energy = 1.7174361e+05
Maximum force = 4.4903098e+02 on atom 172
Yongchul Chung wrote:
Hi all,
I am trying to simulate 100 molecules of n-alkane molecules but keep
receiving LINC errors.
When I completed steepest descent I received following msg:
Steepest Descents converged to Fmax < 500 in 819 steps
Potential Energy = 1.7174361e+05
Maximum force =
delta_t = 0.01
You are using a 10 fs timestep!!! That is way too long. Standard is 2
(with bond constraints).
Yongchul Chung wrote:
Hi all,
I am trying to simulate 100 molecules of n-alkane molecules but keep
receiving LINC errors.
When I completed steepest descent I re
> Stefan Hoorman wrote:
> >
> > > I have included in my simulation some windows past the ~2nm
> distance
> > > between the two groups. The same result occurred, but with a
> longer
> > > separation, the graphic seems to continue rising and the
> > histogram looks
> > > even
Stefan Hoorman wrote:
Hello. Finally came back with the results. Let me again remind you of
what we were talking about. I wanted to obtain the PMF pulling my ligand
out of the protein using umbrella sampling and WHAM. After several
recomendations you asked me to try and simulate the pulling
Hi,
> I registered yesterday and I am logged in, but perhaps I am not
> registered "as contributor"...
>
I added you as a contributor. Thanks for offering to help!
New users are only "viewers" by default to avoid giving instant write
permissions to everyone. People who would
Hi guys,
As Justin pointed out, it was the problem with md simulation blowing up. I
also had coloumbtype=PME and had to switch to cut-off to make my simulation
run faster.
Thanks for all the help.
On Thu, Oct 8, 2009 at 11:44 AM, Jochen Hub wrote:
>
>
>
> delta_t = 0.01
>
> You a
Rossen Apostolov ha scritto:
> Hi,
>> I registered yesterday and I am logged in, but perhaps I am not
>> registered "as contributor"...
>>
> I added you as a contributor. Thanks for offering to help!
>
> New users are only "viewers" by default to avoid giving instant write
>
Yongchul Chung wrote:
Hi guys,
As Justin pointed out, it was the problem with md simulation blowing up.
I also had coloumbtype=PME and had to switch to cut-off to make my
simulation run faster.
And it will be substantially less accurate than using PME. I would say Jochen's
advice is th
Hello gmx users.
I have tried to calculate the enthalpy of vaporization of
toluene liquid, which is about 38kJ/mol (exp. value) using
the OPLS-UA model (7 sites). I generated the toluene topology
adapting a template provided by PRODRG. I have obtained acceptable
value for density and structure of t
Hello gmx users,
I am trying to simulate one protein in solvent with PBC xyz in standard
condition (1 atm, 303K). However since I am using Martini force-field, some
parameters in P-coupling and T-coupling confuse me a lot. Here are two
questions listed below:
1. What is the compressibility
Hi Gromacs users,I am new to Gromacs, and now setting up one very simple
system to test Gromacs+Martini. (one protein with solvent surrounded)
When I run the MD and saw the trajectory, the protein seems go around
randomly, and across the box size. Because Periodic Boundary Condition, it
wil
Pan Wu wrote:
Hello gmx users,
I am trying to simulate one protein in solvent with PBC xyz in
standard condition (1 atm, 303K). However since I am using Martini
force-field, some parameters in P-coupling and T-coupling confuse me a
lot. Here are two questions listed below:
1. What is
you can use trjconv -pbc nojump to take care of that.
On 10/8/09, Pan Wu wrote:
> Hi Gromacs users,I am new to Gromacs, and now setting up one very simple
> system to test Gromacs+Martini. (one protein with solvent surrounded)
> When I run the MD and saw the trajectory, the protein seem
Pan Wu wrote:
Hi Gromacs users,
I am new to Gromacs, and now setting up one very simple system to
test Gromacs+Martini. (one protein with solvent surrounded)
When I run the MD and saw the trajectory, the protein seems go
around randomly, and across the box size.
Whether that's reason
Hi everyone,
I was looking for ways to increase the system size (no. of atoms)
beyond 9 . I read somewhere that there is no inherent constraint
in gromacs on system size rather its because of the format of .gro . I
cant find where i read this but could someone suggest me what to do if
i need t
You don't really need to do anything. Atom number simply starts again.
Catch ya,
Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University
A polar bear is a Cartesian bear that has undergone a polar transformation
-Original Message-
From: gmx-users-boun...@gromacs.org o
> No. My system is a single protein with charged ligand associated with it. But
> why should box size shrink ? In solvated system it does not shrink. What
> effect vacuum could possibly have on it ?
Sounds very much like you have pressure coupling on. Check your .mdp file.
Catch ya,
Dallas Wa
Amit Choubey wrote:
Hi everyone,
I was looking for ways to increase the system size (no. of atoms)
beyond 9 . I read somewhere that there is no inherent constraint
in gromacs on system size rather its because of the format of .gro . I
cant find where i read this but could someone suggest me
Hi all:
I posted this earlier but did not get any help I really need to slove this
issue.
What should be the way to pass a formatted table for the 1-4 interaction
for two or more different groups? Reading page 150 and 180 of manual 4.0,
I
understand user defined potential functions can be
Hi,
As I remember, you can only use one table for 1-4 interactions. Don't know if
it's changed
in the latest version.
Lanyuan
> From: mhrah...@dal.ca
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] user defined potential function for 1-4 interaction
> Date: Thu, 8 Oct 2009 19:10:39 -0300
Gromacs users,
I have a small test system of about 2500 atoms which consists on a few
organic molecules in a box of water. I'm trying to use distance restraints
to keep each molecule apart from each other and I've failed until now.
I'll start by saying that the simulation runs smoothly without usi
João M. Damas wrote:
Gromacs users,
I have a small test system of about 2500 atoms which consists on a few
organic molecules in a box of water. I'm trying to use distance
restraints to keep each molecule apart from each other and I've failed
until now.
I'll start by saying that the simulati
Dear all,
Nobody would like to give some clues for this question, even the
developer of the x2top code?
I use x2top to get topology of a capped carbon nanotube with 168 atoms
using oplsaa force field. The output information about dihedreals shows
as follows.
Before cleaning: 1008 dihedrals
T
Hello
I want to analyze the RMSF fluctuation of each residue of a protein during a
simulation run. I am giving the command
g_rmsf -f md.xtc -s md.tpr -b 4000 -e 6000 -o traj_rmsf.xvg -ox traj_avg.pdb.
Then I am selecting the whole protein for the analysis. I am getting the RMSF
per atom in the
Eudes Fileti wrote:
Hello gmx users.
I have tried to calculate the enthalpy of vaporization of
toluene liquid, which is about 38kJ/mol (exp. value) using
the OPLS-UA model (7 sites). I generated the toluene topology
adapting a template provided by PRODRG. I have obtained acceptable
value for de
Hu Zhongqiao wrote:
Dear all,
Nobody would like to give some clues for this question, even the
developer of the x2top code?
x2top -h
Did you use the -alldih flag? For OPLS like force field all dihedrals
are need, for gromos like ff only one dihedral per bond is kept, that
is why.
I u
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