apt-get install avogadro
http://avogadro.openmolecules.net/wiki/Distribution_Packages
On Wed, Apr 20, 2011 at 10:34 PM, ZHAO Lina wrote:
> There is another free tool (Avogadro) which is pretty easy to handle this
> also.
>
> Try
>
> http://avogadro.openmolecules.net/wiki/G
There is another free tool (Avogadro) which is pretty easy to handle this
also.
Try
http://avogadro.openmolecules.net/wiki/Get_Avogadro
in Build --> Inert ---> Peptides,
Which is very easy to use. you can choose Straight line, beta sheet or alpha
helix or other.
and save as .pdb
lina
--
gmx-
xmgrace gyrate.xvg
On Sat, Apr 16, 2011 at 2:09 PM, Sajad Ahrari wrote:
> hello dear Gromacs users
> i have Gromacs4.5.3 installed on suse11.1.but when i run commands like"
>
> g_gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg" i can't see any
> plot drawn.
> although the command is run
You are really PATIENT waiting for FOUR months for the answers.
Ask the person around you they might be able to provide useful suggestions.
There might be some libs linking problem.
I have never tried the Cygwin,
you may really try "searching" first before "waiting".
lina
P.S if I were you, I
such as residue 288 which is has C
when I tried a C, it's inclusive residue 288.
while tried the ri 288 & a C, it showed me
Group is empty.
Thanks,
On Sun, Mar 27, 2011 at 1:42 PM, ZHAO Lina wrote:
> Hi,
>
> Does the "!" in make_ndx work?
>
> "|" and
Hi,
Does the "!" in make_ndx work?
"|" and "&" work, but seems "!" not work.
I met something weird,
suppose
I choose a C11, which is from ri 1-111.
if use
a C11, the atom is 111
if use
a C11 & ri 1-111, the atom is 111
if use
a C11 & ri 101-111, the atom is 5. Which is expected to be 10, so this
thin the
> cutoff distance, but beyond the cutoff angle. You may got different number
> of hbonds using different cutoff distance and cutoff angle.
> Jianguo
>
> --
> *From:* ZHAO Lina
> *To:* Discussion list for GROMACS users
> *Sent:* Wednesd
@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
0 0 0
200 0 0
400 2 1
600 0 3
800 0 2
1000 1 0
@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
0 0 0
200 0 0
400 2 1
600 0 3
800 0 2
1000 1 0
-cpi state.cpt -append
try to add those two options at the end of your mdrun
lina
On Sun, Mar 13, 2011 at 5:53 AM, mohsen ramezanpour <
ramezanpour.moh...@gmail.com> wrote:
> Dear All
>
> I run a simulation for 4 days.
> Unfortunately it terminated,but not completely,1 steps from 2 h
Hi,
How do get the percentage of the secondary structure propensities of
residues?
seems dssp none such effect?
Thanks for any answers.
lina
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On Mon, Mar 7, 2011 at 11:11 PM, Justin A. Lemkul wrote:
>
>
> ZHAO Lina wrote:
>
>> Hi,
>>
>> I got another question about where does the gromacs looks for the top data
>> file.
>>
>> Specifically,
>>
>> The ~/bin ~/lib and ~/s
Hi,
I got another question about where does the gromacs looks for the top data
file.
Specifically,
The ~/bin ~/lib and ~/share are under my home directory.
the general setting (in .bash_profile) can deal with executables (PATH) and
libraries (LD_LIBRARY_PATH).
How can I set up gromacs looking fo
On Mon, Mar 7, 2011 at 10:45 PM, Justin A. Lemkul wrote:
>
>I'm guessing you have different chain identifiers, i.e. identical
>>chains, just labeled A and B or something?
>>
>>
>> I got four chains. and the .pdb from trjconv do not distinguish those
>> things and don't show chain info.
>>
ATOM397 N ALA48 35.480 52.940 57.920 1.00
0.00
ATOM398 H ALA48 34.740 52.570 57.360 1.00
0.00
ATOM399 CA ALA48 36.190 54.120 57.430 1.00
0.00
ATOM400 CB ALA48 35.900 55.320 58.350 1.00
0.00
ATOM401 C ALA48 37.
On Mon, Mar 7, 2011 at 10:14 PM, Justin A. Lemkul wrote:
>
>
> ZHAO Lina wrote:
>
>> Hi,
>>
>> after added ions, I got a solv_ions.gro.
>>
>> I use trjconv
>>
>> to produce the solv_ions.pdb
>>
>> when I view it in pymo
Hi,
after added ions, I got a solv_ions.gro.
I use trjconv
to produce the solv_ions.pdb
when I view it in pymol.
I showed sequence,
it like
1 2 3 4 6
ODOAOEOROHODOGOOYE
But the solv_ions.pdb looks pretty regular.
my problem is that,
how could I choose the protein parts.
I tri
d, but I don't know why?
>
> Best,
> Majid
>
> --
> *From:* ZHAO Lina
>
> *To:* Discussion list for GROMACS users
> *Sent:* Mon, February 14, 2011 8:04:38 PM
>
> *Subject:* Re: [gmx-users] Gromacs Installation
>
> You are righ
You are right, it's relevant to the shared libs.
but I don't know why you failed in the second attempt if you did a clean
reinstallation.
lina
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: Discussion list for GROMACS users
Subject: Re: RE: [gmx-users] find the relevant structure out
- Original Message -
From: #ZHAO LINA#
Date: Wednesday, November 24, 2010 17:52
Subject: RE: [gmx-users] find the relevant structure out
To: Discussion list for GROMACS users
> Hi,
>
> T
through the argument state=N, where N is
the frame number. If dss doesn't give the assignment you want, you can
also try 'util.ss' that uses a different metric.
Hope it helps,
Tsjerk
>> On 21/11/2010 11:43 PM, #ZHAO LINA# wrote:
>> Hi,
>>
>> I had done 1
]
Sent: Sunday, November 21, 2010 11:58 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] find the relevant structure out
On 21/11/2010 11:43 PM, #ZHAO LINA# wrote:
Hi,
I had done 10ns simulation,
by dssp, can see the beta-sheet appeared very apparently, before it's
alpha-
When I went a bit further, I found it's wrong.
Sorry.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of #ZHAO LINA# [zhao0...@e.ntu.edu.sg]
Sent: Monday, November 22, 2010 4:50 PM
To: Discussion list for GROMACS users
Subjec
I just tried the same way as using NA+, by
genion -s ions.tpr -o protein_solvated_ions.gro -p topol.top -pname K+ -nname
CL- -np Number_of_K
It works, u may do a try.
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Jignesh
_
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Sunday, November 21, 2010 11:58 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] find the relevant structure out
On 21/11/2010 11:43 PM, #ZHAO LIN
Hi,
I had done 10ns simulation,
by dssp, can see the beta-sheet appeared very apparently, before it's
alpha-helix.
there were 5000 frames, I based on the time of the picture got from dssp, I can
guess around which frames is supposed to have those beta sheets.
After I took few frames which I t
: [gmx-users] noxvgr
#ZHAO LINA# wrote:
> I suspect it might mine grace was wrong,
> when I tried to use save as, it has bugs,
> I will check this first.
Exporting to different formats is not done with "Save As" but rather "Print"
(using "Print Setup" to ch
]
Sent: Friday, November 19, 2010 10:15 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] noxvgr
#ZHAO LINA# wrote:
> Hi,
>
> Suppose when I use gyrate, I want the output to be the eps,
>
The only tool that produces .eps files is xpm2ps.
> when I tried -noxvgr -
Hi,
Suppose when I use gyrate, I want the output to be the eps,
when I tried -noxvgr -w
sounds I failed to get.
I do not understand it well.
I can get .xvg picture, and seems the gnuplot not easy to interpret and save it
as .eps or png.
Any idea?
Thanks and best,
lina
--
gmx-users mailing
http://biskit.pasteur.fr/install/applications/dssp
http://oldwww.gromacs.org/pipermail/gmx-users/2009-April/041004.html
http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp?highlight=dssp
HTH,
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, November 05, 2010 9:53 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp
#ZHAO LINA# wrote:
> But right now I noticed something a bit funny,
>
> Try different times,
>
> Back Off! I just backed up ddbGXXqz t
l
2> /dev/null
Failed to execute command: /home/src/DSSP/ -na ddCFya2b ddJZ2M0k > /dev/null 2>
/dev/null
was something wrong with mine DSSP, except path reason.
Thanks,
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org]
rement is that (at least) all "MainChain" atoms be considered. The latest
version of GROMACS seems to handle "Protein" just fine, but older versions did
not. I have no explanation for that, however :)
-Justin
> // Linus Östberg
>
> On Fri, Nov 5, 2010 at 2:08 PM, #ZH
, 2010 at 2:08 PM, #ZHAO LINA# wrote:
> Hi,
>
> Thanks for your response, I modified that path parts when I posted that
> information.
>
> So my environment set was correct.
>
> I just suddenly realize I may not have root privilege there, cause the dssp
> was not
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, November 05, 2010 9:07 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp
#ZHAO LINA# wrote:
> Hi,
>
>
Hi,
Program do_dssp, VERSION 4.0.7
Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471
Fatal error:
Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz > /dev/null 2>
/dev/null
It came out two or three file like ddEPI6I2 and then died like above.
My first tim
http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Olga Ivchenko [olga.ivche...@gmail.com]
Sent: Friday, November 05, 2010 6:02 PM
To: gmx-users@gromacs.org
Subject: [gmx-user
editconf -f peptide.pdb/.gro -o peptide_center_in_simulation_box.gro -center
x/2 y/2 z/2 -box x y z
genbox -cp peptide_center_in_simulation_box.gro -cs spc216.gro -o
they_are_in_the_same_box_now.gro -p topol.top
hth,
lina
From: gmx-users-boun...@gromacs.org [g
I got. -rotate. sorry and thanks.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of #ZHAO LINA# [zhao0...@e.ntu.edu.sg]
Sent: Tuesday, October 26, 2010 8:47 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users
users
Subject: Re: [gmx-users] mirror reflection
editconf -scale -1 -1 -1
On Tue, Oct 26, 2010 at 12:56 PM, Erik Marklund wrote:
> #ZHAO LINA# skrev 2010-10-26 11.46:
>
> Hi,
>
> which can help to get the mirror reflection of a known protein?
>
> Thanks,
>
> lina
>
&
Hi,
which can help to get the mirror reflection of a known protein?
Thanks,
lina
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't
Hi,
I think, started from some gromacs tutorial is a nice ideas and then during
those process you certainly will meet some paper.
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Thomas Schlesier [schl...@uni-mainz.d
Hi,
Fatal error:
[ file protein.itp, line 9 ]:
Atom index (5) in position_restraints out of bounds (1-1).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, October 18, 2010 9:37 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Intrinsically disordered proteins
#ZHAO LINA# wrote:
Hi,
1. For those intrinsically disordered proteins, the sequence is known, how the
simulations will be set up, I mean, the first PDB will be needed, how to get
this one? (Ideally, not necessarily to be practical)
2. suppose I got a PDB, there were several models there, let's say 16, is it
acce
always.
Regarding the nodes ask your administrator how many ppn one node have.
example
suppose if one node has 6 ppn then 12 nodes will have 72ppn which is sufficient
to run md.
hope the above explanation helps you.
Regards
Vinoth
On Wed, Oct 6, 2010 at 2:13 PM, #ZHAO LINA#
mailto:zhao0
Hi,
Estimate for the relative computational load of the PME mesh part: 0.33
How do I set how many nodes I should use?
#PBS -l nodes=12:ppn=4
What if the PME mesh part has different values?
is it okay? Before I did those kind of very blindly, just based on the most
nodes I can use to hopefully
sudo apt-get install grace
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Wednesday, October 06, 2010 11:29 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] Re : installation of
membrane.
#ZHAO LINA# wrote:
> Hi,
>
> When I tried to pack different proteins around the lipids (this protein
> I put it in the position which was nearly going to jump out of the
> lipids, so it's not exactly inserted into it, just very shallow into
> it), I used the vmd to se
Hi,
When I tried to pack different proteins around the lipids (this protein I put
it in the position which was nearly going to jump out of the lipids, so it's
not exactly inserted into it, just very shallow into it), I used the vmd to see
the system.gro, which without being inflated first, I no
.
There are other available too, you should use google to find them. I
have never used any of them so would not like to comment on which to
use, this is up to you to decide after a thorough read of the literature.
Cheers
Tom
#ZHAO LINA# wrote:
> Hi,
>
> Thanks for your answer, I will spend
...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, October 01, 2010 9:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] cholesterol
#ZHAO LINA# wrote:
> Hi,
>
> It will be so bad for me if it really does not exist.
> I wish probably except askin
users
Subject: Re: [gmx-users] cholesterol
#ZHAO LINA# wrote:
> Hi,
>
> Are there some tutorials handling the cholesterol stuff. I read several
> literature but choked in some places.
>
I said this to someone just the other day: if it's not linked at
http://www.gromacs.org/Doc
Hi,
Are there some tutorials handling the cholesterol stuff. I read several
literature but choked in some places.
Thanks with best regards,
lina
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Please search the archive at
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, September 29, 2010 9:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] lipids number
#ZHAO LINA# wrote:
> Hi,
>
> I am not sure someone asked some similar questions before or not.
> >From Prof. Peter Tieleman's website we can get the 128 lipids pdb file.
&g
Hi,
I am not sure someone asked some similar questions before or not.
>From Prof. Peter Tieleman's website we can get the 128 lipids pdb file.
Are there some trick and easy way to multiply those lipids . I mean,
Suppose I need 640 dppc lipids, how can I get those coordinates easily from
those dpp
Are you sure you installed the version 4.0.7?
Hint : your program run on VERSION 4.5.1,
Answer : You know.
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Artur Panczakiewicz [apanczakiew...@gmail.com]
Sent: Thursd
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Position Restraints
#ZHAO LINA# wrote:
> Thanks for your answer.
>
> How can I tell which ones I should restrain? all no-H atoms? in most general
> situations.
For the sake of clarity in the archive, it's probably be
, September 22, 2010 11:15 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Position Restraints
#ZHAO LINA# wrote:
> Hi,
>
> When I used the genrestr to get the posre.itp specially,
> I found it set all atom to be applied to.
> Is that okay? How could I figure out wh
Hi,
When I used the genrestr to get the posre.itp specially,
I found it set all atom to be applied to.
Is that okay? How could I figure out which ones should not be set to.
A little naive questions, but I do do not know.
Thanks with regards,
lina
--
gmx-users mailing listgmx-users@gromacs
Hi,
Just curious, whether the top directory can be split like:
/usr/share/gromacs/top
/usr/local/share/gromacs/top
$HOME/share/gromacs/top
Thanks,
lina
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Please search the archive at
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n the only tool you own is a hammer, every problem begins to resemble a nail.
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of #ZHAO LINA#
Sent: Tuesday, 14 September 2010 2:53 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the g
kville VIC 3010
dallas.war...@monash.edu
+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of #ZHAO LINA#
Sent: Tuesday, 14 September
Hi,
The HO atom type was in the working directory .itp file.
How can I let the grompp work from searching the library of the working
directory, not like this:
grompp -v -f minim.mdp -c dummy.pdb -p topol.top -o dummy.tpr
checking input for internal consistency...
processing topology...
Opening
help!!!
#ZHAO LINA# wrote:
> Make sure your gromacs is the latest version.
> If not, update and try again.
>
The tutorial is specifically written for version 4.0.5, but will be compatible
with any version <4.5. Since the re-organization of the force field
directories, the informatio
Make sure your gromacs is the latest version.
If not, update and try again.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of praba vathy [sumipraba2...@gmail.com]
Sent: Thursday, September 02, 2010 9:06 PM
To: gmx-users@gromacs.org
YourSourceCode/gromacs/src/tools/
If in Linux OS, try
locate g_covar.c
p.s 4.0.3 is not the latest version. why do not try the latest version?
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Carla Jamous [carlajam...@gmail.co
to calculate the distances
- Original Message -
From: #ZHAO LINA#
Date: Thursday, August 26, 2010 15:17
Subject: [gmx-users] How to calculate the distances
To: "gmx-users@gromacs.org"
> Hi all,
>
> I guess the question I'm going to ask probably is a bit sim
Hi all,
I guess the question I'm going to ask probably is a bit simple to those who
know, well. After MD, I got a dimer, how could I get the distance of those two
proteins, the centre of mass distance. In this simulation, there were six
involved, but I only want to calculate the two of them.
.
#ZHAO LINA# wrote:
> Hi,
>
> The problem just like this, in md.log
>
> There are: 130889 Atoms
> splitting topology...
> Walking down the molecule gra
Hi,
The problem just like this, in md.log
There are: 130889 Atoms
splitting topology...
Walking down the molecule graph to make constraint-blocks
There are 43925 charge gro
Try to maximize the intra- and inter-peptide hydrophobic interactions?
I guess it can share the same parameters, just guess, no much idea.
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Vitaly Chaban [vvcha...@gmail.
During your installation, if you use --program-suffix=_mpi, so the mdrun_mpi
will work.
I suggest you to check the nodes of the cluster, probably try pbsnodes, on a
master node no job may be run.
Note that I do not know much about your information, so the (guessing)
suggestion maybe not fit for
remember to change the
pbc = xyz from pbc = no.
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Tsjerk Wassenaar [tsje...@gmail.com]
Sent: Tuesday, June 22, 2010 12:04 PM
To: Discussion list for GROMACS
Check your error message more,
They will tell you which line in which .itp file there is No default Proper
Dih. types.
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Saturday
ter
3 out of 14 complex tests FAILED
Thanks,
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of #ZHAO LINA# [zhao0...@e.ntu.edu.sg]
Sent: Tuesday, June 15, 2010 1:56 PM
To: Discussion list for GROMACS users
Subject: RE:
ble
a nail.
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of #ZHAO LINA#
> Sent: Tuesday, 15 June 2010 3:37 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
>
> The
There is none CRYST1 line in the file try2-water-ions.pdb.
Thanks and regards,
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Dallas B. Warren [dallas.war...@pharm.monash.edu.au]
Sent: Tuesday, June 15, 2010 1:24 PM
sers-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of #ZHAO LINA#
> Sent: Tuesday, 15 June 2010 12:32 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
>
> I used the same commands trying another proteins, but no problems
s.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of #ZHAO LINA#
> Sent:
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, June 14, 2010 10:02 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] the box lengths
#ZHAO LINA#
___
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, June 14, 2010 9:33 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the box lengths
#ZHAO LINA# wrote:
>
Hi,
First time I meet this problem,
ERROR: One of the box lengths is smaller than twice the cut-off length.
Increase the box size or decrease rlist.
I just followed the advice increase the box size, I tried twice in the editconf
about the box size, actually this box is really large enough for t
On 2010-06-03 08.23, #ZHAO LINA# wrote:
> Hi,
>
> When I looked up the manual about the autocorrelation (Chapter 8.5.
> Correlation functions). There is a very general (simple) descriptions. I feel
> I need a bit more deep-relevant references.
> gmx_velacc.c (g_velacc)
Hi,
When I looked up the manual about the autocorrelation (Chapter 8.5. Correlation
functions). There is a very general (simple) descriptions. I feel I need a bit
more deep-relevant references.
gmx_velacc.c (g_velacc) which computes the velocity autocorrelation function,
it's really hard for me
During configuration, there is something about xml.
a functions in analysis
--without-xml do not link to the xml2 library, disallows the
use of certain file formats
1. which file formats did they specify to?
2. Can gromacs handle the PDBML file?
Thanks and regards,
lina
<>-
> lina wrote:
> >> On 6/04/2010 5:39 PM, lina wrote:
> >>> Hi everyone,
> >>>
> >>> Here is the result of the mdrun which was performed on 16cpus. I am
> not
> >>> clear about it, was it due to using MPI reason? or some other
> reasons.
> >>>
> >>> Writing final coordinates.
> >>>
> >>> Average
-body bonded interactions (-rdd) 1.000 nm
multi-body bonded interactions (-rdd) 1.000 nm
Thanks for further suggestion,
lina
#ZHAO LINA# wrote:
> Hi everyone,
>
> I tried to use mdrun to get the .mtx file, but it does not work, I mean...no
> mtx file output.
&g
Hi everyone,
I tried to use mdrun to get the .mtx file, but it does not work, I mean...no
mtx file output.
Below is the command I used in the scripts of my last two trial.
1)
## To run on 16 cpus
#PBS -l nodes=2:ppn=8
## program to run
mpirun -np $NCPUS mdrun_mpi -mtx em.mtx -deffnm em
2)
##
Hi everyone,
I still do not know how to modify it.
Thanks,
Elsa
--
Hi,
Here is the example file I based on to modify,
mpi.sh
#!/bin/bash
#
## Specify the job name
#PBS -N jobname
## Join the standard error and the standard
Hi,
Here is the example file I based on to modify,
mpi.sh
#!/bin/bash
#
## Specify the job name
#PBS -N jobname
## Join the standard error and the standard output into 1 file output
#PBS -j oe
#PBS -V
## To run on 16 cpus
#PBS -l nodes=2:ppn=8
## pre-processing script
cd $PBS_O_WORKDIR
NCPUS=`
Hi,
I tried to run the command
mdrun -deffnm em
on cluster,
blow is the script, but I worried that it might be some place wrong, seems no
files came out after several hours running
Is anyone please help me to modify it, and how can know the process of its
running in the cluster.
Thanks and best
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