No, it does not need to be integer.
With PME it does not matter at all.
With cut-off or reaction-field it is better to have neutral
charge groups when possible, but not at the cost
of making enormous charge groups.
Charge groups should preferable consist of 2, 3 or 4 atoms
which are very close to
>
> On Wed, Nov 19, 2008 at 2:14 PM, Zhao Lifeng <[EMAIL PROTECTED]> wrote:
>
> >
> > Dear all,
> >
> > I encountered a problem in alchemistry free energy calculations:
> >
> > In my simulations a group (A) is to be changed to (B) in a molecule,
> while
> > the atom numbers n(A) is not equal to n(B
I don't know what exactly you are looking for, but normal modes can be
visualized by freewares like Chemcraft, Molekel, etc. Hope it helps.
Marudachalam.
>
>
>
> Hi All,
> I am doing normal mode analysis. After getting the eigen
> frequencies, is
Isabella Daidone wrote:
Hi everybody,
I was wondering if anybody has, and is willing to send me, a .itp file
for cyclohexane with gromos96 parameters.
I searched the list, but could not find any.
I apologize if I've missed it in the list.
Since Gromos96 is a united-atom force field, to cr
Thomas Schlesier wrote:
Hi all,
Sorry that this question is not purely related to GRMOACS. Does anybody
know an free program with which it is possible to save a trajektorie as
a movie? With ngmx and VMD i can visualize the trajektorie but i can not
save it as a movie (with VMD only snapshots ar
Hi Berk,
Should the total charge for one charge group be necessarily an integer, such as
0, 1, -1?
If I understand correctly, the answer is yes. However in this case, the large
charge group always happens except opls-aa force field.
regards,
发件人： Berk Hess
发送时间： 2008-11-20 00:21:07
收件人： D
Hi All,
I am doing normal mode analysis. After getting the eigen frequencies,
is there a way we can visualize the vibrational modes in gromacs. And even how
to know which frequency corresponds to which mode of vibration. I saw that IED
is used
In reading this post, i was hoping that somone can help me locate the
vmd-plugin for pymol. Any suggestions would be greatly appreciated.
-Matthew Danielson-
> Am Mittwoch, den 19.11.2008, 08:36 -0600 schrieb Pete Meyer:
>> One way would be to convert the trajectory to a pdb file, load in
>>
Am Mittwoch, den 19.11.2008, 08:36 -0600 schrieb Pete Meyer:
> One way would be to convert the trajectory to a pdb file, load in
> pymol and generate a series of png images (one for each state with an
> appropriate view), then combine the png's with convert (imagemagick)
> or ffpmeg into a mo
Dear Mark and Arthur, thank you for your reply.
I did what you suggest me and almost everything worked.
I created a topology with the two molecules without bonded parameters
between them and put constrains on two of its atoms.
I did a minimization and a simulation (md integrator).
It worked perfect
0 -6.109 2.742 0.000 0.00 0.00
>>H+0
>>ATOM 13 H UNK 0 -0.774 5.822 0.000 0.00 0.00
>>H+0
>>ATOM 14 H UNK 0 1.893 5.822 0.000 0.00 0.00
>>H+0
>>ATOM 15 H UNK 0
Hi everybody,
I was wondering if anybody has, and is willing to send me, a .itp file for
cyclohexane with gromos96 parameters.
I searched the list, but could not find any.
I apologize if I've missed it in the list.
Thank you very much,
Isabella
___
On Wed, Nov 19, 2008 at 5:49 AM, Mark Abraham <[EMAIL PROTECTED]> wrote:
> xianghong qi wrote:
>>
>> Dear all:
>>
>> I have a simple system which has two methane molecules with water. Now I
>> need turn off the intermolecular interactions between these two methanes and
>> just run
>> simulation. S
Thanks, Mark. I will check the manual.
-Xianghong Qi
On Wed, Nov 19, 2008 at 11:39 AM, Mark Abraham <[EMAIL PROTECTED]>wrote:
> xianghong qi wrote:
>
>> Hi, Mark,
>>
>> Which method can work with exclusion? Could you give me some hints for
>> that? Thanks again.
>>
>
> I'm not your free teacher.
xianghong qi wrote:
Hi, Mark,
Which method can work with exclusion? Could you give me some hints for
that? Thanks again.
I'm not your free teacher... :-) You need to have a much better working
knowledge of MD than one such that you need to ask that question.
Certainly with your present know
Hi, Mark,
Which method can work with exclusion? Could you give me some hints for that?
Thanks again.
-Xianghong Qi
On Wed, Nov 19, 2008 at 10:41 AM, xianghong qi <[EMAIL PROTECTED]>wrote:
> Thanks so much for your nice explaination, Mark.
> -Xianghong Qi
>
>
> On Wed, Nov 19, 2008 at 6:01 AM, Ma
Hi,
The charge groups "only" affect the neighbor searching,
which in practice means they affect everything.
In Gromacs atoms in two different charge groups will only interactions
when the center of geometry of the two charge groups is within rlist.
The worst case scenario, which has happend to
Hello All
Recently I have figured out the biggest problem that made my system unstable.
I have parameterized a molecule pretty similar to octane. A single
charge group used to be assigned to this molecule. With 1 nm cut-off
distance for LJ interaction and the direct space for electrostatic
interac
Bernhard Knapp wrote:
thanks for the hints but unfortunately i still can not get the molecule
running. i tried with both prodrg server and x2top but with limited success:
in the first case i generate the gro.pdb and .top file via the
webinterface [1] of prodrg by pasting my coordinate file int
thanks for the hints but unfortunately i still can not get the molecule
running. i tried with both prodrg server and x2top but with limited success:
in the first case i generate the gro.pdb and .top file via the
webinterface [1] of prodrg by pasting my coordinate file into the
textbox. then i
/Thomas Schlesier wrote:
>// Hi all,
>// Sorry that this question is not purely related to GRMOACS. Does anybody
>// know an free program with which it is possible to save a trajektorie as
>// a movie? With ngmx and VMD i can visualize the trajektorie but i can not
>// save it as a movie (with VMD
Thanks so much for your nice explaination, Mark.
-Xianghong Qi
On Wed, Nov 19, 2008 at 6:01 AM, Mark Abraham <[EMAIL PROTECTED]>wrote:
> xianghong qi wrote:
>
>> Hi, Mark:
>> I put the energygrps = Methane1 Methane2 into mdp file.
>> grompp gives one warning:
>> WARNING 1 [file conf.top, line 4
On Wed, Nov 19, 2008 at 2:14 PM, Zhao Lifeng <[EMAIL PROTECTED]> wrote:
>
> Dear all,
>
> I encountered a problem in alchemistry free energy calculations:
>
> In my simulations a group (A) is to be changed to (B) in a molecule, while
> the atom numbers n(A) is not equal to n(B).
> A scheme is to i
Thomas Schlesier wrote:
Hi all,
Sorry that this question is not purely related to GRMOACS. Does anybody
know an free program with which it is possible to save a trajektorie as
a movie? With ngmx and VMD i can visualize the trajektorie but i can not
save it as a movie (with VMD only snapshots are
One way would be to convert the trajectory to a pdb file, load in
pymol and generate a series of png images (one for each state with an
appropriate view), then combine the png's with convert (imagemagick)
or ffpmeg into a movie.
Doubtless there's a more elegant way to do it, though.
Pete
Hi,
That is strange.
This looks like a different box size than you mailed yesterday.
Could you mail me the tpr file that caused this error?
Berk
Date: Wed, 19 Nov 2008 14:22:29 +
From: [EMAIL PROTECTED]
Subject: RE: [gmx-users] gromacs 4.0.2 error in continuation to triclinic skew
err
Hello,
the run didn't even start and I got this:
Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Minimum cell size due to bonded interactions: 1.000 nm
Scaling the initial minimum size with 1/0.8 (option -dds)
Dear all,
I encountered a problem in alchemistry free energy calculations:
In my simulations a group (A) is to be changed to (B) in a molecule, while
the atom numbers n(A) is not equal to n(B).
A scheme is to include both A and B in the same topology file and switch
on/off the B/A charges and vdw
Hi,
I don't know what the reason for the large LJ14 distance is,
but this will be over 3 bonds, not over 1 bond (which I guess the 0.154 is
that you mentioned).
This has nothing to do with the parallelization.
I would use 4.0.2, since there are many small issues fixed that were in 4.0.0.
In 4.0.
Hi all,
Sorry that this question is not purely related to GRMOACS. Does anybody
know an free program with which it is possible to save a trajektorie as
a movie? With ngmx and VMD i can visualize the trajektorie but i can not
save it as a movie (with VMD only snapshots are possible).
Thanks for answ
Hello,
thank you for all your responses up to now. The thing is getting much more
clearer.
Yet, as far as the distance is concerned, this is a little bit worrying,
because I have bonded interactions no more than 0.154 nm away. So a distance
more than a whole nm I think that should be very long
Yes, it is possible by deveoping your own topology. Pdb2gmx is not suitable for
that purpose.
It would be helpful to check out the documentation resources and manual, e.g.
http://wiki.gromacs.org/index.php/FAQs
x2top and the prodgr web-server might be some good starting points.
Andreas
>
Dear users
I would like to perform a MD simulation of Sedoheptulose (C7H14O7) via
Gromacs. But already during pdb2gmx it comes up with:
"Residue 'UNK' not found in residue topology database" which is
obviously clear since sedoheptulose is not an amino acid. Is it somehow
possible to simulate t
Dear Mark,
Thank you very much for the link!
It's a good idea, imho, to put this link to the documentation section because
it is nearly impossible to find it without asking here.
Semen
- Original Message
From: Mark Abraham <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Se
Thank you for the fast reply - I will try to find out what works best for me.
All the best,
Jan Götze
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.
[EMAIL PROTECTED] wrote:
Hello everyone,
I would like to know if there is a tool for grabbing all individual
interactions of a system (analogous to the tinker tool "analyze"). I
skimmed through the available tools, however, I was unable to find one
which performs that function.
Technically,
Semen Esilevsky wrote:
Dear All,
Where can I find documentation about the pull code in Gromacs 4.0? As far as I understand old style of setting up pulling simulations in separate file does not work any more, but I can't figure out how to transfer pulling params correctly to mdp file.
Any help is
Hi,
Currently there is a beta 4.0 manual on ftp.gromacs.org.
The mdp options can also be found in:
share/html/online/mdp_opt.html
Berk
> Date: Wed, 19 Nov 2008 03:33:47 -0800
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Pulling in 4.0 - Any documentation?
>
>
Hello everyone,
I would like to know if there is a tool for grabbing all individual
interactions of a system (analogous to the tinker tool "analyze"). I
skimmed through the available tools, however, I was unable to find one
which performs that function.
Technically, it should be enough to
Dear All,
Where can I find documentation about the pull code in Gromacs 4.0? As far as I
understand old style of setting up pulling simulations in separate file does
not work any more, but I can't figure out how to transfer pulling params
correctly to mdp file.
Any help is appreciated!
P.S. Pr
Suman Chakrabarty wrote:
On Wed, Nov 19, 2008 at 5:57 AM, Mark Abraham <[EMAIL PROTECTED]> wrote:
Suman Chakrabarty wrote:
Now when I try to follow his script posted at
http://www.gromacs.org/pipermail/gmx-users/2008-November/037973.html ,
checking for int... yes
checking size of int... con
On Wed, Nov 19, 2008 at 5:57 AM, Mark Abraham <[EMAIL PROTECTED]> wrote:
> Suman Chakrabarty wrote:
>
>> Now when I try to follow his script posted at
>> http://www.gromacs.org/pipermail/gmx-users/2008-November/037973.html ,
>> I find that it does not work for me. Error is:
>>
>> checking for mpxlc
Hi,
I am new to gromacs and have a pretty basic question. I am using gromacs-3.3.3
to simulate glycine crystal growth. My system consists of glycine crystal
surrounded by a solution of glycine in water (system size: 4.28 by 5.76 by 3.27
nm^3). I have been trying to find appropriate values for t
sarbani chattopadhyay wrote:
Hi,
I do understand that reducing the number of replicas will limit my
temperature space,
but gromacs 3.3.2 can run 1 replica per node. Thus having 4 nodes , I
can have only 4
replicas. Thus in case I want to span a temperature space of 313K to
333K using onl
xianghong qi wrote:
Hi, Mark:
I put the energygrps = Methane1 Methane2 into mdp file.
grompp gives one warning:
WARNING 1 [file conf.top, line 47]:
Can not exclude the lattice Coulomb energy between energy groups
then grompp terminated.
Could you give me a hint about his problem? Thanks
Hi,
You can run as many replica's you want on one machine.
One "gromacs node" does not have to correspond to a physical
node or core.
If you have 4 nodes, you can use for instance mpirun -np 12
to have 3 replica's per physical node.
Usually this will just work, in some cases you might need to
mod
Hi,
I do understand that reducing the number of replicas will limit my
temperature space,
but gromacs 3.3.2 can run 1 replica per node. Thus having 4 nodes , I can have
only 4
replicas. Thus in case I want to span a temperature space of 313K to 333K using
only 4
replicas, is there any
Hi, Mark:
I put the energygrps = Methane1 Methane2 into mdp file.
grompp gives one warning:
WARNING 1 [file conf.top, line 47]:
Can not exclude the lattice Coulomb energy between energy groups
then grompp terminated.
Could you give me a hint about his problem? Thanks.
-Xianghong Qi
On Wed, N
Thanks, Mark.
-Xianghong Qi
On Wed, Nov 19, 2008 at 3:46 AM, Mark Abraham <[EMAIL PROTECTED]>wrote:
> xianghong qi wrote:
>
>> Hi, Mark:
>> for these two cases
>> energygrp_excl = Methane1 Methane2
>> and energygrp_excl = methane1 methane2
>> I got same error: methane1(or M
xianghong qi wrote:
Hi, Mark:
for these two cases
energygrp_excl = Methane1 Methane2
and
energygrp_excl = methane1 methane2
I got same error: methane1(or Methane1 ) is not energy group.
OK, so now that it's a group, you need it to be an energy group - see
energygrps
Hi, Mark:
for these two cases
energygrp_excl = Methane1 Methane2
and
energygrp_excl = methane1 methane2
I got same error: methane1(or Methane1 ) is not energy group.
Thanks so much.
-Xianghong Qi
On Wed, Nov 19, 2008 at 3:25 AM, Mark Abraham <[EMAIL PROTECTED]>wrote:
>
Hi,
The LJ-14 interaction is a two-body interaction,
one of which is apparently at a distance longer than the non-bonded cut-off.
mdrun determines the communication distances when starting
the simulation, see the md.log file for details.
Apparently all your bonded interactions are initially withi
xianghong qi wrote:
and index file was makde from command make_ndx, I named the two methanes
as methane1 and methane2.
So what's different above and below? :-)
energygrp_excl = Methane1 Methane2
This is why it's important to look at, and report what you *have* done,
not what you
sarbani chattopadhyay wrote:
Hi everyone,
I will like to do Replica exchange simulation on a
peptide. We have a single
machine with 4 cpus and the gromacs3.3.2 is installed.
Thus I will be able to select only 4 temperature values. I came across
the "T-REMD" caculator
for te
Hi, Mark,
I use the command: grompp -f md.mdp -c eq2.gro -p conf.top -n md.ndx -o
md.tpr -t eq2.trr
and index file was makde from command make_ndx, I named the two methanes as
methane1 and methane2.
and my mdp file is :
integrator = sd
ld_seed = -1
; start time and
xianghong qi wrote:
Hi, Mark:
I made the index file and call two methanes as methane1 and methane2 ,
then I set energygrp_excl = methane1 methane2, but when I run grompp, it
said methane1 is not an energy group. What do you understand this
problem? Thanks. -Xianghong Qi
You haven't done wh
Hi everyone,
I will like to do Replica exchange simulation on a peptide.
We have a single
machine with 4 cpus and the gromacs3.3.2 is installed.
Thus I will be able to select only 4 temperature values. I came across the
"T-REMD" caculator
for temperature distributions . H
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