Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?

[ZHAO Lina]

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/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
>
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Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?

[ZHAO Lina]

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
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Re: [gmx-users] drawing the plots

[ZHAO Lina]

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 with no error.
> by the way i have the package "package xmgrace-5.1.21-27.91.x86_64" already 
> installed.
> thanks!
> sajad
>
> 
>
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Re: [gmx-users] Installation error

[ZHAO Lina]

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 would try on linux.
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[gmx-users] Re: make_ndx

[ZHAO Lina]

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 "&" 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
> situation is wrong.
> if use
> a C11 & ri 1-100, the atom is 100, which is right.
>
> I want to know  how can I use "!" to exclude some group?
>
> This mistake is reproducible and I didn't figure it out (Even I examined
> the .gro).
>
> Thanks for any suggestion.
>
> lina
>
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[gmx-users] make_ndx

[ZHAO Lina]

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
situation is wrong.
if use
a C11 & ri 1-100, the atom is 100, which is right.

I want to know  how can I use "!" to exclude some group?

This mistake is reproducible and I didn't figure it out (Even I examined the
.gro).

Thanks for any suggestion.

lina
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Re: [gmx-users] Re: g_hbond output

[ZHAO Lina]

 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

Here is my question, since there is already one bond formed, then why there
is none pairs in 1000?


On Wed, Mar 16, 2011 at 3:16 PM, Jianguo Li  wrote:

> If I understand correctly, $2 is the number of hydrogen bonds defined by
> cutoff distance and the cutoff angle. $3 is the number of pairs within 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:* Wednesday, 16 March 2011 13:33:57
> *Subject:* [gmx-users] Re: g_hbond output
>
> @ 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
> :
>  5   3   2
>
> Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if
> the $3 means pairs.
>
> I tried pymol, and on the last frame,
> there were 4 hydrogen bonds, between 7 residues. it's different from here 3
> 2
>
> Thanks and sorry for last email without my realization it sent.
>
> lina
>
>
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[gmx-users] Re: g_hbond output

[ZHAO Lina]

@ 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
:
 5   3   2

Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if
the $3 means pairs.

I tried pymol, and on the last frame,
there were 4 hydrogen bonds, between 7 residues. it's different from here 3
2

Thanks and sorry for last email without my realization it sent.

lina
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[gmx-users] g_hbond output

[ZHAO Lina]

@ 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
:
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Re: [gmx-users] terminated but not completely

[ZHAO Lina]

-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 has
> done.
> Is there any way to run the continue of my files?
> Thanks in advance for your guidances
> Best Regards
>
>
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[gmx-users] secondary structure propensities of residues

[ZHAO Lina]

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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Re: [gmx-users] where does the gromacs looks for the top data file.

[ZHAO Lina]

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 ~/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 for top data files in ~/share
>>
>> After in topol.top I put
>> ; Include forcefield parameters
>> #include "/home/lina/share/gromacs/top/gromos43a1.ff/forcefield.itp"
>> I still have following problems.
>>
>> Program grompp, VERSION 4.5.3
>> Source code file: futil.c, line: 897
>>
>> Fatal error:
>> Library file residuetypes.dat not found in current dir nor in default
>> directories.
>> (You can set the directories to search with the GMXLIB path variable)
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
> Gromacs searches first in the working directory, then in $GMXLIB, then in
> any other directories included in the .mdp file "include =
> -I/whatever/directory."
>
> Presumably, if you installed everything in /home/lina/, then you can source
> GMXRC in ~/bin and the environment will be configured for you.
>
>
$ source GMXRC
-bash: /home/lina/bin/GMXRC.bash: No such file or directory
[lina@pineapple scripts]$ pwd
/home/lina/src/build/gromacs-4.5.3/scripts

I'm confused. I have no problem with what under ~/bin and ~/lib but
something wrong with the ~/share.

lina
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[gmx-users] where does the gromacs looks for the top data file.

[ZHAO Lina]

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 for top data files in ~/share

After in topol.top I put
; Include forcefield parameters
#include "/home/lina/share/gromacs/top/gromos43a1.ff/forcefield.itp"
I still have following problems.

Program grompp, VERSION 4.5.3
Source code file: futil.c, line: 897

Fatal error:
Library file residuetypes.dat not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path variable)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Thanks,

lina
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Re: [gmx-users] select in pymol after trjconv

[ZHAO Lina]

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.
>>
>> Do you have some nice way to view .gro in pymol. (compare VMD I am a bit
>> familiar with pymol)
>>
>>
> Renumber using genconf.  You should be able to select consecutive residues
> in this way.  Otherwise, use a couple quick text editor tricks to write in
> chain identifiers to make selection easy.
>

genconf works so perfect here.

Thanks again!

lina



>
> -Justin
>
>  Thanks again,
>>
>> lina
>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] select in pymol after trjconv

[ZHAO Lina]

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  37.690  53.840  57.260  1.00
0.00
ATOM402  O1  ALA48  38.120  52.590  57.580  1.00
0.00
ATOM403  O2  ALA48  38.460  54.860  56.810  1.00
0.00
ATOM404  N   ASP 1   7.960  12.190  74.660  1.00
0.00
ATOM405  H1  ASP 1   8.090  11.710  75.530  1.00
0.00
ATOM406  H2  ASP 1   7.210  12.840  74.760  1.00
0.00
ATOM407  H3  ASP 1   7.730  11.520  73.950  1.00
0.00
ATOM408  CA  ASP 1   9.190  12.900  74.290  1.00
0.00
ATOM409  CB  ASP 1  10.390  11.940  74.180  1.00
0.00
ATOM410  CG  ASP 1  10.860  11.380  75.510  1.00
0.00
ATOM411  OD1 ASP 1  10.420  11.850  76.560  1.00
0.00
ATOM412  OD2 ASP 1  11.880  10.480  75.450  1.00
0.00
ATOM413  C   ASP 1   9.000  13.630  72.970  1.00
0.00
ATOM414  O   ASP 1   8.580  13.010  71.990  1.00  0.00



>>
>
> 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.

Do you have some nice way to view .gro in pymol. (compare VMD I am a bit
familiar with pymol)

Thanks again,

lina
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Re: [gmx-users] select in pymol after trjconv

[ZHAO Lina]

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 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 tried the select protein, resi 1-48
>> some waters are inclusive.
>>
>>
> Do you have a very large system?  If so, PDB format can only handle a fixed
> number of digits in the residue and atom numbering fields, so the numbering
> of your waters restarts from zero.  Such is the limitation when dealing with
> .pdb files.
>

Kind of large.
I was wrong before, the newly-produced solv_ions.pdb is not regular.
Before those chains numbered in sequence.
now different chains numbered from 1-48 1-48 again, former is 1-96 in .gro.


>
> If you just need to make selections in PyMOL, strip the water out of the
> file first.
>

It's short, the protein part, I did it manually, but the "show cartoon"
failed to show all, only show first 1-48.

I guess I gotta modify the .pdb a little.

Thanks for your answering.

lina


>
> -Justin
>
>
>  Thanks for any suggestion.
>>
>> lina
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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[gmx-users] select in pymol after trjconv

[ZHAO Lina]

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 tried the select protein, resi 1-48
some waters are inclusive.

Thanks for any suggestion.

lina
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Re: [gmx-users] Gromacs Installation

[ZHAO Lina]

"clean" reinstallation.

make uninstall
make distclean
rm -r 

from source re-install it again.

lina

On Tue, Feb 15, 2011 at 12:39 PM, majid hasan wrote:

> Okay. Actually, second time, I over-worte the first installation. I mean I
> didn't uninstall the first one, I just ran the whole process again starting
> from fftw$./configure. I am not sure if that is all right, I just did it to
> find out the problem. In the third attempt (without issuing --enable-shared
> anywher), I again over-wrote the gromacs installation files, and this went
> well. It worked, 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 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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Re: [gmx-users] Gromacs Installation

[ZHAO Lina]

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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RE: [gmx-users] find the relevant structure out

[#ZHAO LINA#]

I do not know how to extract some special frames out (professionally),
so I just simply use vim to take the relevant models out and put into a new pdb 
file.
Are there some good ways to extract one or two frames at the end of those whole 
frames?

Base on your answering, now I start to suspect I might make something wrong 
cause I did it really clumsily.

Thanks for your answering,

lina


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Wednesday, November 24, 2010 3:19 PM
To: 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,
>
> Thanks for your answering.
>
> Due to the difference in assignment, so I wonder which one I
> should build a bit much more faith on?
>
> I read (by eyes) the ss.xpm produced by do_dssp, and find the
> relevant resi out which showed as beta-sheet, but in pymol, it's
> really so standard alpha-helix, when I tried "alter" in pymol to
> show the beat-sheet as the way Justine mentioned in early email,
> it's really look weird.


It's rather more likely that you're comparing two different (parts of) 
structures, than one secondary structure algorithm assigns sheet and one 
assigns helix to the same part of the same structure. Is the residue/atom 
numbering consistent. What does do_dssp say about the frame you cut out to give 
to pymol?


Mark

>
> I noticed lots of paper they use DSSP to say something.
>
> Thanks,
>
> lina
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-
> boun...@gromacs.org] on behalf of Tsjerk Wassenaar [tsje...@gmail.com]
> Sent: Wednesday, November 24, 2010 1:27 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] find the relevant structure out
>
> Hi,
>
> > Visualization software can sometimes assign the secondary
> structure incorrectly.
>
> There has been an interesting discussion on this on the Pymol user
> list years ago (http://www.mail-archive.com/pymol-
> us...@lists.sourceforge.net/msg01574.html).Secondary structure
> assignment is foremost human defined. You can use
> different metrics to obtain assignments, and should be careful
> to take
> any one of them as 'correct'. For instance, it makes a difference
> whether you assign three types (helical, sheet, loop), as Pymol does,
> or like seven types, as DSSP does.
>
> In pymol you can set the secondary structure type manually, but
> I find
> that the internal command 'dss' usually does a good job. Note
> that it
> only works on one frame and then uses the assignment for that
> frame on
> all of them, although there may be a workaround (I'll check; something
> with discrete_states). The frame to use for the assignment can be
> given to the 'dss' command 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 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 thought might be
> representive, but under
> >> pymol, show cartoon, there is none beta sheet at all. There
> were 5000 frames,
> >> I really do not know which one is most representive.
> >>
> >> Or maybe some parts I understand wrong.
> >>
> >> Thanks for any advice and if I am wrong please let me know,
> >>
> >> We've really no idea of the detail of what you've done, so
> can't guess. Just
> >> about anything could be the problem - all the way from "you
> are looking at
> >> the wrong files", to "pymol's definition of a beta sheet
> doesn't agree with
> >> dssp".
> >>
> >> If you can't report the command lines you used easily, then
> your method was
> >> not reproducible enough, or not recorded well enough :-)
> >>
> >> Mark
> >>
> >
> >
> > ==

RE: [gmx-users] find the relevant structure out

[#ZHAO LINA#]

Hi,

Thanks for your answering. 

Due to the difference in assignment, so I wonder which one I should build a bit 
much more faith on? 

I read (by eyes) the ss.xpm produced by do_dssp, and find the relevant resi out 
which showed as beta-sheet, but in pymol, it's really so standard alpha-helix, 
when I tried "alter" in pymol to show the beat-sheet as the way Justine 
mentioned in early email, it's really look weird.

I noticed lots of paper they use DSSP to say something. 

Thanks, 

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Tsjerk Wassenaar [tsje...@gmail.com]
Sent: Wednesday, November 24, 2010 1:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] find the relevant structure out

Hi,

> Visualization software can sometimes assign the secondary structure 
> incorrectly.

There has been an interesting discussion on this on the Pymol user
list years ago 
(http://www.mail-archive.com/pymol-us...@lists.sourceforge.net/msg01574.html).
Secondary structure assignment is foremost human defined. You can use
different metrics to obtain assignments, and should be careful to take
any one of them as 'correct'. For instance, it makes a difference
whether you assign three types (helical, sheet, loop), as Pymol does,
or like seven types, as DSSP does.

In pymol you can set the secondary structure type manually, but I find
that the internal command 'dss' usually does a good job. Note that it
only works on one frame and then uses the assignment for that frame on
all of them, although there may be a workaround (I'll check; something
with discrete_states). The frame to use for the assignment can be
given to the 'dss' command 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 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 thought might be representive, but under
>> pymol, show cartoon, there is none beta sheet at all. There were 5000 frames,
>> I really do not know which one is most representive.
>>
>> Or maybe some parts I understand wrong.
>>
>> Thanks for any advice and if I am wrong please let me know,
>>
>> We've really no idea of the detail of what you've done, so can't guess. Just
>> about anything could be the problem - all the way from "you are looking at
>> the wrong files", to "pymol's definition of a beta sheet doesn't agree with
>> dssp".
>>
>> If you can't report the command lines you used easily, then your method was
>> not reproducible enough, or not recorded well enough :-)
>>
>> Mark
>>
>
>
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> 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 post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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RE: [gmx-users] find the relevant structure out

[#ZHAO LINA#]

I really do not know how to get those beta-sheet structures out,
or maybe by which ways?

Any clues are warmly welcomed and appreciated.

lina

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 LINA# wrote:
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 thought might be representive, but under pymol, 
show cartoon, there is none beta sheet at all. There were 5000 frames, I really 
do not know which one is most representive.

Or maybe some parts I understand wrong.

Thanks for any advice and if I am wrong please let me know,

We've really no idea of the detail of what you've done, so can't guess. Just 
about anything could be the problem - all the way from "you are looking at the 
wrong files", to "pymol's definition of a beta sheet doesn't agree with dssp".

If you can't report the command lines you used easily, then your method was not 
reproducible enough, or not recorded well enough :-)

Mark
-- 
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RE: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

[#ZHAO LINA#]

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
Subject: RE: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

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 Patel [jbp...@gmail.com]
Sent: Monday, November 22, 2010 3:57 PM
To: gromacs user
Subject: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

Dear all,

Can anybody tell me how to incorporate potassium ion parameters in GROMACS for 
GROMOS53a6 forcefield.

Thanking you in anticipation.

With regards,
Jignesh


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RE: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

[#ZHAO LINA#]

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 Patel [jbp...@gmail.com]
Sent: Monday, November 22, 2010 3:57 PM
To: gromacs user
Subject: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

Dear all,

Can anybody tell me how to incorporate potassium ion parameters in GROMACS for 
GROMOS53a6 forcefield.

Thanking you in anticipation.

With regards,
Jignesh


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RE: [gmx-users] find the relevant structure out

[#ZHAO LINA#]

do_dssp -f traj.xtc -s topol.tpr -o ss.xpm

trjconv -s topol.tpr -f traj.xtc -o protein.pdb -pbc nojump

Took several frames, here, such as model 1000, model 3000 and model 5000, and 
named as 1000.pbd, 3000.pdb and 5000.pdb

pymol 3000.pdb

intra_fit protein and (name c,n,ca)

show cartoon

all the way from "you are looking at the wrong files", to "pymol's definition 
of a beta sheet doesn't agree with dssp".

what are those files I should have looked for, and how could I find a better 
way to show those beta-sheet out?

Thanks,

lina

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 LINA# wrote:
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 thought might be representive, but under pymol, 
show cartoon, there is none beta sheet at all. There were 5000 frames, I really 
do not know which one is most representive.

Or maybe some parts I understand wrong.

Thanks for any advice and if I am wrong please let me know,

We've really no idea of the detail of what you've done, so can't guess. Just 
about anything could be the problem - all the way from "you are looking at the 
wrong files", to "pymol's definition of a beta sheet doesn't agree with dssp".

If you can't report the command lines you used easily, then your method was not 
reproducible enough, or not recorded well enough :-)

Mark
-- 
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[gmx-users] find the relevant structure out

[#ZHAO LINA#]

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 thought might be representive, but under pymol, 
show cartoon, there is none beta sheet at all. There were 5000 frames, I really 
do not know which one is most representive.

Or maybe some parts I understand wrong.

Thanks for any advice and if I am wrong please let me know,

lina
-- 
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RE: [gmx-users] noxvgr

[#ZHAO LINA#]

It works (cool). Thanks for both of you. 

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, November 19, 2010 10:23 PM
To: Discussion list for GROMACS users
Subject: Re: [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 choose the proper format).  Simply saving your plot
creates an XmGrace file that only it can load.

-Justin

>
> Thanks for your answering.
>
> lina
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
> of Justin A. Lemkul [jalem...@vt.edu]
> 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 -w
>>
>
> Is -noxvgr even a correct option?  It seems like if you want non-formatted
> output, you should use "-xvg none" in the command line.
>
> If you just want an .eps output file of the plot, use the normal XmGrace
> formatting (leave the command line -xvg alone) and save the output in that
> format.  XmGrace should be capable of saving an .eps, and if not, you can take
> whatever image file format it gives you into Gimp and convert it.
>
> -Justin
>
>> 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
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> 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 post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] noxvgr

[#ZHAO LINA#]

I suspect it might mine grace was wrong,
when I tried to use save as, it has bugs,
I will check this first.

Thanks for your answering.

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
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 -w
>

Is -noxvgr even a correct option?  It seems like if you want non-formatted
output, you should use "-xvg none" in the command line.

If you just want an .eps output file of the plot, use the normal XmGrace
formatting (leave the command line -xvg alone) and save the output in that
format.  XmGrace should be capable of saving an .eps, and if not, you can take
whatever image file format it gives you into Gimp and convert it.

-Justin

> 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
>

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] noxvgr

[#ZHAO LINA#]

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
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RE: [gmx-users] DSSP error

[#ZHAO LINA#]

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...@gromacs.org] on behalf 
of ahmet yıldırım [ahmedo...@gmail.com]
Sent: Wednesday, November 10, 2010 10:02 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] DSSP error

Hi,

I installed in /usr/local/bin the DSSP program. And I set the environment 
variable with a command such as “export DSSP=/usr/local/bin/dssp”.
a...@ubuntu:/Desktop/work# do_dssp -s run.tpr -f run.xtc
...
Selected 1: 'Protein'
There are 164 residues in your selected group
Opening library file /usr/share/gromacs/top/ss.map
Reading frame   0 time0.000
Back Off! I just backed up dduigjCp to ./#dduigjCp.1#

---
Program do_dssp, VERSION 4.0.5
Source code file: ../../../../src/tools/do_dssp.c, line: 471

Fatal error:
Failed to execute command: /usr/local/bin/dssp -na dduigjCp ddDsSuzR > 
/dev/null 2> /dev/null
---
"Jesus Not Only Saves, He Also Frequently Makes Backups." (Myron Bradshaw)

What should I do?

Thanks in advance

--
Ahmet YILDIRIM
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RE: [gmx-users] dssp

[#ZHAO LINA#]

Last email the paths really look messy, because as I said before,

I modified by mine hand before posted it. 

Sorry about that. I did export the path before. :-)

Thanks,

lina

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 9:53 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 to ./#ddbGXXqz.1#
>
> ---
> Program do_dssp, VERSION 4.0.7
> Source code file: /home/src/gromacs-4.0.7-mbh/src/tools/do_dssp.c, line: 471
>
> Fatal error:
> Failed to execute command: /home/zhao0139/src/ball/DSSP/ -na ddbGXXqz 
> ddEflfyy > /dev/null 2> /dev/null
>
>
> Failed to execute command: /home/srcl/DSSP/ -na ddtWJ3ry ddR1Hjkz > /dev/null 
> 2> /dev/null
> Failed to execute command: /home/srcl/DSSP/ -na ddhF6K9M ddcDcvax > /dev/null 
> 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.
>

I still think you're setting your DSSP environment variable wrong.  Please
consult the link I posted before - you have to point DSSP to the *actual
executable* not the directory that contains it, i.e.:

WRONG: export DSSP=/opt/bin

RIGHT: export DSSP=/opt/bin/dssp

-Justin

> Thanks,
>
> lina
> ____
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
> of #ZHAO LINA# [zhao0...@e.ntu.edu.sg]
> Sent: Friday, November 05, 2010 9:35 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] dssp
>
> Hi,
>
> 1. There is no wrong in mine executable path, it's mine fault that I MODIFIED 
> the "real and true" path to a simple way as it showed "pathTo..." before I 
> posted.
>
> 2. seems not about root things, cause every body can write and read to/from 
> /dev/null
>
> 3. I will try another time ?!
>
> Thanks,
>
> lina
> 
> 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 9:32 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] dssp
>
> Linus Östberg wrote:
>> What did you try to do? To use dssp, you must select entire residues,
>> e.g. 1 (protein). That error sounds a bit like my problem when trying
>> to do dssp using only the backbone.
>>
>
> The original message indicates the wrong executable was called.  The reasons
> might still be unclear at this point, but instead of executing "dssp," do_dssp
> was executing "pathToDSSP" instead.
>
> The group for analysis is also debatable.  I have seen hangs and seg faults 
> when
> "Protein" is selected, and other times it works fine.  The only absolute
> requirement 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, #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 small, not in mine personal computer, there are in some other 
>>> places.
>>>
>>> lina
>>>
>>> 
>>> 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,
>>>>
>>>> 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.
>

RE: [gmx-users] dssp

[#ZHAO LINA#]

But right now I noticed something a bit funny,

Try different times,

Back Off! I just backed up ddbGXXqz to ./#ddbGXXqz.1#

---
Program do_dssp, VERSION 4.0.7
Source code file: /home/src/gromacs-4.0.7-mbh/src/tools/do_dssp.c, line: 471

Fatal error:
Failed to execute command: /home/zhao0139/src/ball/DSSP/ -na ddbGXXqz ddEflfyy 
> /dev/null 2> /dev/null


Failed to execute command: /home/srcl/DSSP/ -na ddtWJ3ry ddR1Hjkz > /dev/null 
2> /dev/null
Failed to execute command: /home/srcl/DSSP/ -na ddhF6K9M ddcDcvax > /dev/null 
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] on behalf 
of #ZHAO LINA# [zhao0...@e.ntu.edu.sg]
Sent: Friday, November 05, 2010 9:35 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] dssp

Hi,

1. There is no wrong in mine executable path, it's mine fault that I MODIFIED 
the "real and true" path to a simple way as it showed "pathTo..." before I 
posted.

2. seems not about root things, cause every body can write and read to/from 
/dev/null

3. I will try another time ?!

Thanks,

lina

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 9:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp

Linus Östberg wrote:
> What did you try to do? To use dssp, you must select entire residues,
> e.g. 1 (protein). That error sounds a bit like my problem when trying
> to do dssp using only the backbone.
>

The original message indicates the wrong executable was called.  The reasons
might still be unclear at this point, but instead of executing "dssp," do_dssp
was executing "pathToDSSP" instead.

The group for analysis is also debatable.  I have seen hangs and seg faults when
"Protein" is selected, and other times it works fine.  The only absolute
requirement 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, #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 small, not in mine personal computer, there are in some other places.
>>
>> lina
>>
>> 
>> 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,
>>>
>>> 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 time try dssp, so do not know how to examine it.
>>>
>> Your DSSP environment variable is set incorrectly.  do_dssp is trying to call
>> "pathToDSSP" as the executable.
>>
>> http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
>>
>> Note that you should substitute a meaningful PATH on your system, not 
>> something
>> like "pathToDSSP."
>>
>> -Justin
>>
>>> Thanks for any advice,
>>>
>>> lina
>>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

RE: [gmx-users] dssp

[#ZHAO LINA#]

Hi,

1. There is no wrong in mine executable path, it's mine fault that I MODIFIED 
the "real and true" path to a simple way as it showed "pathTo..." before I 
posted.

2. seems not about root things, cause every body can write and read to/from 
/dev/null

3. I will try another time ?! 

Thanks,

lina

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 9:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp

Linus Östberg wrote:
> What did you try to do? To use dssp, you must select entire residues,
> e.g. 1 (protein). That error sounds a bit like my problem when trying
> to do dssp using only the backbone.
>

The original message indicates the wrong executable was called.  The reasons
might still be unclear at this point, but instead of executing "dssp," do_dssp
was executing "pathToDSSP" instead.

The group for analysis is also debatable.  I have seen hangs and seg faults when
"Protein" is selected, and other times it works fine.  The only absolute
requirement 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, #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 small, not in mine personal computer, there are in some other places.
>>
>> lina
>>
>> 
>> 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,
>>>
>>> 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 time try dssp, so do not know how to examine it.
>>>
>> Your DSSP environment variable is set incorrectly.  do_dssp is trying to call
>> "pathToDSSP" as the executable.
>>
>> http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
>>
>> Note that you should substitute a meaningful PATH on your system, not 
>> something
>> like "pathToDSSP."
>>
>> -Justin
>>
>>> Thanks for any advice,
>>>
>>> lina
>>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> 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 post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> 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 post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.or

RE: [gmx-users] dssp

[#ZHAO LINA#]

I did choose 1 protein when it asked me to choose.

Thanks for your answering, I may try on my desktop another time.

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Linus Östberg [bio...@talavis.eu]
Sent: Friday, November 05, 2010 9:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] dssp

What did you try to do? To use dssp, you must select entire residues,
e.g. 1 (protein). That error sounds a bit like my problem when trying
to do dssp using only the backbone.

// Linus Östberg

On Fri, Nov 5, 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 small, not in mine personal computer, there are in some other places.
>
> lina
>
> 
> 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,
>>
>> 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 time try dssp, so do not know how to examine it.
>>
>
> Your DSSP environment variable is set incorrectly.  do_dssp is trying to call
> "pathToDSSP" as the executable.
>
> http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
>
> Note that you should substitute a meaningful PATH on your system, not 
> something
> like "pathToDSSP."
>
> -Justin
>
>> Thanks for any advice,
>>
>> lina
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> 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 post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing listgmx-users@gromacs.org
> 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 post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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RE: [gmx-users] dssp

[#ZHAO LINA#]

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 small, not in mine personal computer, there are in some other places.

lina


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,
>
> 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 time try dssp, so do not know how to examine it.
>

Your DSSP environment variable is set incorrectly.  do_dssp is trying to call
"pathToDSSP" as the executable.

http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp

Note that you should substitute a meaningful PATH on your system, not something
like "pathToDSSP."

-Justin

> Thanks for any advice,
>
> lina
>

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Please search the archive at 
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[gmx-users] dssp

[#ZHAO LINA#]

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 time try dssp, so do not know how to examine it.

Thanks for any advice,

lina
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RE: [gmx-users] which force file has parameters for creatine md simulations

[#ZHAO LINA#]

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-users] which force file has parameters for creatine md simulations

Dear All,

I want to do molecular dynamics with creatine. But I can not transform creatine 
pdb file downloaded from drugbank to gromac topology file using command: 
pdb2gmx -f

Please can you write me if there is a force filed for which creatine parameters 
are already exist and I can use this forcefield for simulations?

I have attached pdb file.

Thanks in advance,
Olga
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RE: [gmx-users] center peptide in simulation box

[#ZHAO LINA#]

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 [gmx-users-boun...@gromacs.org] on behalf 
of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Thursday, November 04, 2010 5:53 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] center peptide in simulation box

On 3/11/2010 9:04 PM, leila karami wrote:
Dear Mark Abraham

In March 2010, In reply to question about [center peptide in simulation box], 
You answered:

OK, well keep playing with the trjconv options and choosing sensible groups for 
centering until you find something that pleases you. You may
need to do two different trjconv operations - one to center the peptide and one 
to group the waters in the same periodic cell as the peptide.


I want to know how can I do last (group the waters in the same periodic cell as 
the peptide)?


I'd find the answer to this by reading trjconv -h and experimenting :-)

Mark
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RE: [gmx-users] mirror reflection

[#ZHAO LINA#]

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] mirror reflection

Cool, but what if the mirror was set on y=-x in the x-y plane.


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Tsjerk Wassenaar [tsje...@gmail.com]
Sent: Tuesday, October 26, 2010 8:12 PM
To: Discussion list for GROMACS 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
>
> If it's just one conformation, then I'd just write a script that multiplies
> all x-, y- or z-coordinates by -1 in a pdb- or gro-file. Is that what you're
> after, or is it something more intricate?
>
> Cheers,
>
> --
> ---
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 4537fax: +46 18 511 755
> er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/
>
> --
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--
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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RE: [gmx-users] mirror reflection

[#ZHAO LINA#]

Cool, but what if the mirror was set on y=-x in the x-y plane. 


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Tsjerk Wassenaar [tsje...@gmail.com]
Sent: Tuesday, October 26, 2010 8:12 PM
To: Discussion list for GROMACS 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
>
> If it's just one conformation, then I'd just write a script that multiplies
> all x-, y- or z-coordinates by -1 in a pdb- or gro-file. Is that what you're
> after, or is it something more intricate?
>
> Cheers,
>
> --
> ---
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 4537fax: +46 18 511 755
> er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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[gmx-users] mirror reflection

[#ZHAO LINA#]

 Hi,

which can help to get the mirror reflection of a known protein?

Thanks,

lina
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RE: [gmx-users] Re: published paper related to protein simulation, using gromacs

[#ZHAO LINA#]

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.de]
Sent: Thursday, October 21, 2010 7:45 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: published paper related to protein simulation, using 
gromacs

Hi,
use ISI Web of Knowledge or scholar.google, search for 'protein +
gromacs' and you should get tons of results.
Greetings
Thomas


> Date: Thu, 21 Oct 2010 13:29:11 +0300
> From: ahmet y?ld?r?m
> Subject: [gmx-users] published paper related to protein simulation
>   using   gromacs
> To: Discussion list for GROMACS users
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Gromacs users,
>
> I am new user Gromacs. I want to study on protein simulation using gromacs.
> If possible, Can you send a few articles on the protein simulation using
> Gromacs?For example, I downloaded from Protein Data Base the PDB extension
> file of any protein. What is the purpose of protein simulation?What is
> commonly the forcefied used for protein simulation? Which parameters are
> calculated?... To answer these questions, I need the articles/papers written
> in this area.
> I will be happy if you help
>
> Thanks in advance
>
>

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[gmx-users] position_restraints

[#ZHAO LINA#]

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" section to the right molecule.

Thanks for any clue. The part belongs to the one I want to restraints. I mean, 
the molecule is right.

Thanks,

lina
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RE: [gmx-users] Intrinsically disordered proteins

[#ZHAO LINA#]

Hi, 

1. Thanks for the webpage you provided, I noticed there is a avogadro there, 
and  right now coincidently I have a question relevant to the avogadro,

When I tried the avogadro-packmol-extensions, I had installed the avogadro and 
packmol well, 
but I do not know

where the avogadro plugins/modules can be put ?
I tried the put the packmolextension.so under usr/lib/avogadro/1_0/extensions/ 
but seems not work,

Might someone has tried and knew the answer, actually  I had asked on the other 
place, but none feedback.

2.  Wow, it's going to be lots of works. 

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)
>

http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources

> 2. suppose I got a PDB, there were several models there, let's say 16,
> is it acceptable to just take one, say model 1?
>

Making an arbitrary choice is not a good idea.  You have to justify that the
model you selected is in some way representative of the ensemble.  You could do
that by demonstrating that your simulation overlapped the configuration space of
the ensemble in the PDB file, i.e. sampled all the expected configurations, thus
the starting structure was not an inappropriate bias.

-Justin

> Thanks for any answering,
>
> lina
>

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Intrinsically disordered proteins

[#ZHAO LINA#]

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 
acceptable to just take one, say model 1?

Thanks for any answering,

lina

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RE: [gmx-users] How can I best setup the nodes number

[#ZHAO LINA#]

I think I know how many ppn one nodes have. :-)

My question was that the number of ppn has something to do with the PME mesh 
part number or not?

Why sometimes I had a big load imbalance.

Thanks and best regards,

lina


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of vinothkumar mohanakrishnan [kmvin...@gmail.com]
Sent: Wednesday, October 06, 2010 4:48 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How can I best setup the nodes number

I think the PME mesh part is ok and it should be less than 0.5 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...@e.ntu.edu.sg>> wrote:
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 run quickly.

Thanks and best regards,

lina

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[gmx-users] How can I best setup the nodes number

[#ZHAO LINA#]

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 run quickly.

Thanks and best regards,

lina
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RE: [gmx-users] Re : installation of gromacs in windows on cygwin

[#ZHAO LINA#]

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 gromacs in windows on cygwin

bharat gupta wrote:
> thanks for ur help.. I have figured out the problem and not installation
> is going on .. I want to know one more thing that xmgrace which is
> required for plotting the data .. how can we install it as I have
> searched on google .. but  I am not able to get the correct link
>

The first Google result for "xmgrace" is the site you want, I don't know what
else to tell you.

http://plasma-gate.weizmann.ac.il/Grace/

Follow whatever documentation they provide to install it.

-Justin

> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46...@yahoo.com 
>

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] protein embedded into membrane.

[#ZHAO LINA#]

Thanks for your answering. I will check those further later.

The unclear question was that, to the final .gro. How can I tell it that one 
(protein embedded in membrane) is okay or nice, so I can continue.

based on area per lipids, or after EM ... are there some criteria?

Thanks and best regards,

lina 


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, October 04, 2010 11:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] protein embedded into 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 see the system.gro, which without being inflated
> first, I noticed
> some warnings like this:
>
> Warning) Unusual bond between residues:  40 (protein) and 491 (none)
> Warning) Unusual bond between residues:  40 (protein) and 491 (none)
> Warning) Unusual bond between residues:  40 (protein) and 491 (none)
>
> when I removed those residues such as 491 (none), not protein ones,
> those warning disappeared.
>

VMD is detecting close contacts, not actual bonds, but since its heuristic
algorithm tells it there are bonds, then you get these warnings.  Perhaps a
simple EM will resolve them, but maybe not.

> I noticed on Justine's tutorial, there were 26 iterations of scaling
> down. I did those iterations step by step manually before and cost me
> nearly 40 mind-not-running minutes to finish, but later I spent crazy 2
> hours or more to write a short and clumsy script to save mine 40 mins
> work in the future. This is not the point.  The point was that, are
> there some shortcuts? I wonder whether I could avoid doing those
> inflategro first, and then shrink and energy minimization also being
> avoided by simply removed those lipids (I know I still need a final EM).
> or,

What is presented in the tutorial is simply one way to build a membrane protein
system.  If you have an easier case, then as long as you can justify your
methods, do what you see fit.  Perhaps the iterations of InflateGRO are, in your
case, unnecessary.  There is also a new tool called g_membed that might be
useful.  It is far more automated than InflateGRO, but I have never used it 
myself.

> Can we locally inflated those membrane and then locally packed them
> together. Very local, or maybe just simply removed those lipids.
>

Not to my knowledge, unless you write this program yourself.

> How could I make sure the removal ones are going to be nice, from which
> sides I should check.
>

I don't understand what you're asking for here.

-Justin

> Thanks and best regards,
>
> lina
>
> p.s  To avoid a very trivial description, I put some background
> information below, thanks for your time.
>
> from Tieleman's website
> http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis
>
> and Justine's webpage
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
>
>  I tried pack the lipids around the protein, no doubt followed perfectly
> based on the tutorial before.
>
>

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] protein embedded into membrane.

[#ZHAO LINA#]

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 noticed
some warnings like this:

Warning) Unusual bond between residues:  40 (protein) and 491 (none)
Warning) Unusual bond between residues:  40 (protein) and 491 (none)
Warning) Unusual bond between residues:  40 (protein) and 491 (none)

when I removed those residues such as 491 (none), not protein ones, those 
warning disappeared.

I noticed on Justine's tutorial, there were 26 iterations of scaling down. I 
did those iterations step by step manually before and cost me nearly 40 
mind-not-running minutes to finish, but later I spent crazy 2 hours or more to 
write a short and clumsy script to save mine 40 mins work in the future. This 
is not the point.  The point was that, are there some shortcuts? I wonder 
whether I could avoid doing those inflategro first, and then shrink and energy 
minimization also being avoided by simply removed those lipids (I know I still 
need a final EM).
or,
Can we locally inflated those membrane and then locally packed them together. 
Very local, or maybe just simply removed those lipids.

How could I make sure the removal ones are going to be nice, from which sides I 
should check.

Thanks and best regards,

lina

p.s  To avoid a very trivial description, I put some background information 
below, thanks for your time.

from Tieleman's website
http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis

and Justine's webpage
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html

 I tried pack the lipids around the protein, no doubt followed perfectly based 
on the tutorial before.


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RE: [gmx-users] cholesterol

[#ZHAO LINA#]

Thanks for your clue.

I found the very interesting paper about that force field.

Thanks again,

lina



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Thomas Piggot [t.pig...@soton.ac.uk]
Sent: Friday, October 01, 2010 9:22 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] cholesterol

I can think of a few cholesterol topologies just off the top of my head:

GROMOS43A1-S3 forcefield has an entry for cholesterol

There is a stream file for cholesterol available for use with the CHARMM
forcefields.

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 some time to figure it out.
>
> By the way, any links or literature or something relevant to it warmly 
> welcome to introduce them to me.
>
> Best regards,
>
> lina
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@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 asking Dr. google, someone else will be able to 
>> provide me some links.
>> I once just wanted to see some examples how they handled its topology even I 
>> got one from
>> PRODRG server, but it has problems later. Not so much in those specific 
>> simulations yet, just beginning stage.
>>
>
> If your problem is with deriving parameters, then do a thorough literature
> search.  Simulations with cholesterol have been done with numerous force 
> fields,
> so parameterization methodology and/or suitable parameters should be 
> available.
>
> -Justin
>
>> lina
>>
>> 
>> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on 
>> behalf of Justin A. Lemkul [jalem...@vt.edu]
>> Sent: Friday, October 01, 2010 8:35 PM
>> To: Discussion list for GROMACS 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/Documentation/Tutorials or you can't find it with 
>> Google,
>> it probably doesn't exist.
>>
>> What's more, "handling the cholesterol stuff" doesn't really lend itself to
>> getting useful help.  What are you trying to do?  Derive parameters?  Build a
>> membrane?  A micelle?  An LDL complex?
>>
>> -Justin
>>
>>> Thanks with best regards,
>>>
>>> lina
>>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
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> Can't post? Read http://w

RE: [gmx-users] cholesterol

[#ZHAO LINA#]

Hi,

Thanks for your answer, I will spend some time to figure it out. 

By the way, any links or literature or something relevant to it warmly welcome 
to introduce them to me.

Best regards,

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@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 asking Dr. google, someone else will be able to 
> provide me some links.
> I once just wanted to see some examples how they handled its topology even I 
> got one from
> PRODRG server, but it has problems later. Not so much in those specific 
> simulations yet, just beginning stage.
>

If your problem is with deriving parameters, then do a thorough literature
search.  Simulations with cholesterol have been done with numerous force fields,
so parameterization methodology and/or suitable parameters should be available.

-Justin

> lina
>
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
> of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Friday, October 01, 2010 8:35 PM
> To: Discussion list for GROMACS 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/Documentation/Tutorials or you can't find it with 
> Google,
> it probably doesn't exist.
>
> What's more, "handling the cholesterol stuff" doesn't really lend itself to
> getting useful help.  What are you trying to do?  Derive parameters?  Build a
> membrane?  A micelle?  An LDL complex?
>
> -Justin
>
>> Thanks with best regards,
>>
>> lina
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> 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 post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] cholesterol

[#ZHAO LINA#]

Hi, 

It will be so bad for me if it really does not exist. 
I wish probably except asking Dr. google, someone else will be able to provide 
me some links.
I once just wanted to see some examples how they handled its topology even I 
got one from 
PRODRG server, but it has problems later. Not so much in those specific 
simulations yet, just beginning stage.   

lina


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, October 01, 2010 8:35 PM
To: Discussion list for GROMACS 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/Documentation/Tutorials or you can't find it with Google,
it probably doesn't exist.

What's more, "handling the cholesterol stuff" doesn't really lend itself to
getting useful help.  What are you trying to do?  Derive parameters?  Build a
membrane?  A micelle?  An LDL complex?

-Justin

> Thanks with best regards,
>
> lina
>

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] cholesterol

[#ZHAO LINA#]

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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RE: [gmx-users] lipids number

[#ZHAO LINA#]

I have a vague impression about that, seems someone asked similar things before.

I will do a try and see.

Thanks,

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Wednesday, 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.
> 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 dppc128 ones.
>

You can make integer multiples of a box with genconf -nbox.  Otherwise use
genbox -cs dppc128.pdb -box (x y z) until you get a system of appropriate size.
  There was a very similar post yesterday about this same topic.  I would
suggest you have a look at the information Chris Neale posted about the
specifics of box size (genbox caveats) and the need for proper equilibration.

-Justin

> Thanks and best regards,
>
> lina
>

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] lipids number

[#ZHAO LINA#]

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 dppc128 ones.

Thanks and best regards,

lina
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RE: [gmx-users] Getting started - Peptide

[#ZHAO LINA#]

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: Thursday, September 23, 2010 10:02 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Getting started - Peptide

Dear Gromacs Users,

I'm a freshman and would like to lear how to use GROMACS in my
research starting from tutorial. I've just installed the newest
version and try to repeat all of the steps from the chapter that
describes the preparation of Ribonuclease A to MD simulation. In my
case it is not possible, unfortunatelly. The grompp program crashes
such a way:

---
Program grompp, VERSION 4.5.1
Source code file: toppush.c, line: 1987

Fatal error:
No such moleculetype SOL
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I tried to install GROMACS on other machine with different Linux
distribution but the error in grompp was the same.
What is important, I installed version 4.0.7 and it works well! I
don't have any idea what is going on.
Does anyone have a similar problem?

Regards,
Artur
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RE: [gmx-users] Position Restraints

[#ZHAO LINA#]

Thanks for your answer again.

I will restrain the heavy atoms only first.

Best regards,

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Wednesday, September 22, 2010 11:43 AM
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 best to avoid broad
generalizations.  People can easily stumble upon a post and take it way out of
context.  A "general situation" might encompass a lot.  I will reiterate that if
you want to recapitulate the behavior of pdb2gmx with respect to typical
biomolecules, you should choose all non-H atoms.

If you have some other specialized application, I can make no recommendation,
nor can anyone else, in the absence of a more thorough description.

-Justin

>
> lina
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
> of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Wednesday, 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 which ones should not be set to.
>>
>> A little naive questions, but I do do not know.
>
> The answer depends on your needs.  When running genrestr without an index 
> file,
> you can choose from any of the default groups.  If you provide an index file,
> any group can be chosen.
>
> The default behavior of pdb2gmx is to generate a posre.itp file that restrains
> all heavy (non-H) atoms.  You can do the same with genrestr if you want, but
> again, the atoms you want to restrain depend on your goals.
>
> -Justin
>
>> Thanks with regards,
>>
>> lina
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> 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 post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] Position Restraints

[#ZHAO LINA#]

Thanks for your answer.

How can I tell which ones I should restrain? all no-H atoms? in most general 
situations.

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Wednesday, 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 which ones should not be set to.
>
> A little naive questions, but I do do not know.

The answer depends on your needs.  When running genrestr without an index file,
you can choose from any of the default groups.  If you provide an index file,
any group can be chosen.

The default behavior of pdb2gmx is to generate a posre.itp file that restrains
all heavy (non-H) atoms.  You can do the same with genrestr if you want, but
again, the atoms you want to restrain depend on your goals.

-Justin

>
> Thanks with regards,
>
> lina
>

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Position Restraints

[#ZHAO LINA#]

 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
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[gmx-users] top directory can be split or not?

[#ZHAO LINA#]

 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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RE: [gmx-users] how to let the grompp finding library fromworkingdirectory first.

[#ZHAO LINA#]

The HO.itp is nothing wrong with this.

I found the answer from last part of this page 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html).

It's a bit trivial and I will test it later.

Thanks again for you time.

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Dallas Warren [dallas.war...@monash.edu]
Sent: Tuesday, September 14, 2010 1:35 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library 
fromworkingdirectory first.

What is the contents of the HO.itp file?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville 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 2010 2:53 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library 
fromworkingdirectory first.

Yes.

I did it already. But it did not work.
in topol.top file,
;Include topology
#include "HO.itp"

Thanks,

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Dallas Warren [dallas.war...@monash.edu]
Sent: Tuesday, September 14, 2010 12:48 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library from 
workingdirectory first.
What is the contents of your topol.top and HO.itp file?  Does the topol.top 
“include” the HO.itp in it?

To have an “included topology file” (.itp) file processed by grompp, it has to 
be directed to it.  This is typically done by using a #include “HO.itp” line 
within the topol.top file.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville 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 2010 2:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] how to let the grompp finding library from 
workingdirectory first.

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 library file /usr/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations

---
Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/toppush.c, line: 947

Fatal error:
Atomtype HO not found
---

Do I need add something in minim.mdp? Or maybe just some parts wrong I do not 
realise.

Thanks and best regards,

lina
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RE: [gmx-users] how to let the grompp finding library from workingdirectory first.

[#ZHAO LINA#]

Yes.

I did it already. But it did not work.
in topol.top file,
;Include topology
#include "HO.itp"

Thanks,

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Dallas Warren [dallas.war...@monash.edu]
Sent: Tuesday, September 14, 2010 12:48 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library from 
workingdirectory first.

What is the contents of your topol.top and HO.itp file?  Does the topol.top 
“include” the HO.itp in it?

To have an “included topology file” (.itp) file processed by grompp, it has to 
be directed to it.  This is typically done by using a #include “HO.itp” line 
within the topol.top file.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville 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 2010 2:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] how to let the grompp finding library from 
workingdirectory first.

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 library file /usr/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations

---
Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/toppush.c, line: 947

Fatal error:
Atomtype HO not found
---

Do I need add something in minim.mdp? Or maybe just some parts wrong I do not 
realise.

Thanks and best regards,

lina
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[gmx-users] how to let the grompp finding library from working directory first.

[#ZHAO LINA#]

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 library file /usr/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations

---
Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/toppush.c, line: 947

Fatal error:
Atomtype HO not found
---

Do I need add something in minim.mdp? Or maybe just some parts wrong I do not 
realise.

Thanks and best regards,

lina
-- 
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RE: [gmx-users] Need help!!!

[#ZHAO LINA#]

But it's a bit trivial to modify those things if you just following those steps 
by steps.
Using the latest version can save lots of works.

By the way, thanks for the website, I once followed that too (nearly step by 
step also).

Thanks with best regards,

lina

P.S actually you can upgrade your website also. ^_^ 

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Thursday, September 02, 2010 9:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Need 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 information provided in the tutorial is not correct.

I would recommend not upgrading until the OP has sorted out the problem and can
then (maybe) work out the appropriate translation to the version 4.5.x scheme.

-Justin

>
> 
> *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
> *Subject:* [gmx-users] Need help!!!
>
> Hi,
>
> I am using simulation for a membrane protein.
> So i have downloaded the dppc.pdb along with it's topology files.
> I have used the following steps for the simulation (Based on the link:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html).
>
> We have used the commands and steps as described in the above link.
> But we have got a fatal error (Atom type C not found) while running this
> command,
>
> grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tp <http://em.tp>
>
> I cant sort out this problem.
> Please anybody help me to sort out this problem.
> Awaiting for your valuable replies.
>
> Praba
>

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] Need help!!!

[#ZHAO LINA#]

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
Subject: [gmx-users] Need help!!!

Hi,

I am using simulation for a membrane protein.
So i have downloaded the dppc.pdb along with it's topology files.
I have used the following steps for the simulation (Based on the link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html).

We have used the commands and steps as described in the above link.
But we have got a fatal error (Atom type C not found) while running this 
command,

grompp -f mini.mdp -c dppc128.gro -p topol_dppc.top -o em.tp

I cant sort out this problem.
Please anybody help me to sort out this problem.
Awaiting for your valuable replies.

Praba
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RE: [gmx-users] g_covar

[#ZHAO LINA#]

 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.com]
Sent: Monday, August 30, 2010 8:53 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] g_covar

Hi everyone,

please I'm using gromacs 4.0.3, and I want to see the program g_covar, except 
that I have it in binary file and I want to see the C program in text format.

Please how can I have access to it?

Thank you
Carla
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RE: [gmx-users] How to calculate the distances

[#ZHAO LINA#]

Dear Mark,

It works.

Thanks,

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Thursday, August 26, 2010 1:48 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How 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 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.

Probably g_dist. See section 7.4 of the manual for some clues, and then the man 
pages of the individual tools for more information.

Mark

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[gmx-users] How to calculate the distances

[#ZHAO LINA#]

 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.

Thanks,

lina
-- 
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RE: [gmx-users] the mdrun choked or maybe braked.

[#ZHAO LINA#]

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, August 13, 2010 7:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the mdrun choked or maybe braked.

#ZHAO LINA# wrote:
>  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 group borders and 43271 shake borders
> There are 43271 total borders
> Division over nodes in atoms:
> 93489348934893519348935193489351
> 93489351
> 9348935193489350
> Walking down the molecule graph to make constraint-blocks
> CPU=  0, lastcg= 3245, targetcg=25208, myshift=8
> CPU=  1, lastcg= 6361, targetcg=28324, myshift=8
> CPU=  2, lastcg= 9477, targetcg=31440, myshift=8
> CPU=  3, lastcg=12594, targetcg=34557, myshift=8
> CPU=  4, lastcg=15710, targetcg=37673, myshift=8
> CPU=  5, lastcg=18827, targetcg=40790, myshift=8
> CPU=  6, lastcg=21943, targetcg=43906, myshift=7
> CPU=  7, lastcg=25060, targetcg= 3098, myshift=7
> CPU=  8, lastcg=28176, targetcg= 6214, myshift=7
> CPU=  9, lastcg=31293, targetcg= 9331, myshift=7
> CPU= 10, lastcg=34409, targetcg=12447, myshift=7
> CPU= 11, lastcg=37526, targetcg=15564, myshift=7
> CPU= 12, lastcg=40642, targetcg=18680, myshift=7
> CPU= 13, lastcg=43924, targetcg=21962, myshift=8
> pd->shift =   8, pd->bshift=  0
> Division of bonded forces over processors
> CPU  0 1 2 3 4 5 6 7 8
> 910
>   111213
> G96ANGLES 2376 0 0 0 0 0 0 0 0
> 0 0
>0 0 0
> PDIHS  774 0 0 0 0 0 0 0 0
> 0 0
>0 0 0
> IDIHS  852 0 0 0 0 0 0 0 0
> 0 0
>0 0 0
> LJ14  2436 0 0 0 0 0 0 0 0
> 0 0
>0 0 0
> CONSTR1614 0 0 0 0 0 0 0 0
> 0 0
>0 0 0
> SETTLE2586  3116  3116  3117  3116  3117  3116  3117  3116
> 3117  3116
> 3117  3116  3034
> Workload division
> nnodes:  14
> pd->shift:8
> pd->bshift:   0
> Nodeid   atom0   #atom cg0   #cg
>  0   09348   0  3246
>  1934893483246  3116
>  2   1869693486362  3116
>  3   2804493519478  3117
>  4   373959348   12595  3116
>  5   467439351   15711  3117
>  6   560949348   18828  3116
>  7   654429351   21944  3117
>  8   747939348   25061  3116
>  9   841419351   28177  3117
> 10   934929348   31294  3116
> 11  1028409351   34410  3117
> 12  1121919348   37527  3116
> 13  1215399350   40643  3282
>
> Max number of connections per atom is 27
> Total number of connections is 32076
> Max number of graph edges per atom is 4
> Total number of graph edges is 13572
> Initial temperature: 303.113 K
>
> Started mdrun on node 0 Fri Aug 13 14:38:46 2010
>
>Step   Time Lambda
>   00.00.0
>
> Grid: 10 x 45 x 10 cells
>Energies (kJ/mol)
>G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
> 2.96784e+031.16372e+039.89996e+02   -1.07478e+012.63019e+04
> LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)   RF excl.
> 3.11913e+05   -8.40005e+03   -2.19295e+06   -1.39523e+04   -3.36479e+04
>   PotentialKinetic En.   Total EnergyTemperature Pressure (bar)
>-1.90563e+063.31599e+05   -1.57403e+063.0e+021.07070e+01
>   Cons. rmsd ()
> 2.63140e-05
> 
>
> Nothing more at the end,
> I changed the 16 cores to 14 cores, still has the same problem. And when
> I checked the status, it showed me it's finished.
>

Please provide more information.  It mdrun stopped, it must have had a reason.
Please provide your .mdp file, description of the system, and what you did as
far as energy minimization and/or equilibration prior to whatever this run was
doing.  If mdrun fails, there's always a reason, and it would be ver

[gmx-users] the mdrun choked or maybe braked.

[#ZHAO LINA#]

 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 group borders and 43271 shake borders
There are 43271 total borders
Division over nodes in atoms:
9348934893489351934893519348935193489351
9348935193489350
Walking down the molecule graph to make constraint-blocks
CPU=  0, lastcg= 3245, targetcg=25208, myshift=8
CPU=  1, lastcg= 6361, targetcg=28324, myshift=8
CPU=  2, lastcg= 9477, targetcg=31440, myshift=8
CPU=  3, lastcg=12594, targetcg=34557, myshift=8
CPU=  4, lastcg=15710, targetcg=37673, myshift=8
CPU=  5, lastcg=18827, targetcg=40790, myshift=8
CPU=  6, lastcg=21943, targetcg=43906, myshift=7
CPU=  7, lastcg=25060, targetcg= 3098, myshift=7
CPU=  8, lastcg=28176, targetcg= 6214, myshift=7
CPU=  9, lastcg=31293, targetcg= 9331, myshift=7
CPU= 10, lastcg=34409, targetcg=12447, myshift=7
CPU= 11, lastcg=37526, targetcg=15564, myshift=7
CPU= 12, lastcg=40642, targetcg=18680, myshift=7
CPU= 13, lastcg=43924, targetcg=21962, myshift=8
pd->shift =   8, pd->bshift=  0
Division of bonded forces over processors
CPU  0 1 2 3 4 5 6 7 8 910
  111213
G96ANGLES 2376 0 0 0 0 0 0 0 0 0 0
   0 0 0
PDIHS  774 0 0 0 0 0 0 0 0 0 0
   0 0 0
IDIHS  852 0 0 0 0 0 0 0 0 0 0
   0 0 0
LJ14  2436 0 0 0 0 0 0 0 0 0 0
   0 0 0
CONSTR1614 0 0 0 0 0 0 0 0 0 0
   0 0 0
SETTLE2586  3116  3116  3117  3116  3117  3116  3117  3116  3117  3116
3117  3116  3034
Workload division
nnodes:  14
pd->shift:8
pd->bshift:   0
Nodeid   atom0   #atom cg0   #cg
 0   09348   0  3246
 1934893483246  3116
 2   1869693486362  3116
 3   2804493519478  3117
 4   373959348   12595  3116
 5   467439351   15711  3117
 6   560949348   18828  3116
 7   654429351   21944  3117
 8   747939348   25061  3116
 9   841419351   28177  3117
10   934929348   31294  3116
11  1028409351   34410  3117
12  1121919348   37527  3116
13  1215399350   40643  3282

Max number of connections per atom is 27
Total number of connections is 32076
Max number of graph edges per atom is 4
Total number of graph edges is 13572
Initial temperature: 303.113 K

Started mdrun on node 0 Fri Aug 13 14:38:46 2010

   Step   Time Lambda
  00.00.0

Grid: 10 x 45 x 10 cells
   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
2.96784e+031.16372e+039.89996e+02   -1.07478e+012.63019e+04
LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)   RF excl.
3.11913e+05   -8.40005e+03   -2.19295e+06   -1.39523e+04   -3.36479e+04
  PotentialKinetic En.   Total EnergyTemperature Pressure (bar)
   -1.90563e+063.31599e+05   -1.57403e+063.0e+021.07070e+01
  Cons. rmsd ()
2.63140e-05


Nothing more at the end,
I changed the 16 cores to 14 cores, still has the same problem. And when I 
checked the status, it showed me it's finished.

Thanks for any advice,

lina


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RE: [gmx-users] Re: dimer simulation

[#ZHAO LINA#]

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.com]
Sent: Wednesday, August 11, 2010 1:37 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: dimer simulation

I think your choice should depend on what bonds you expect between the
two monomers forming a dimer.

--
Dr. Vitaly Chaban


> Dear gmx-users
> I want to simulate a protein which biological function defined by dimer
> formation. I need to simulate this protein in dimer as well as in
> monomeric form to solve my objectives. I am using Gromacs-4.0.4 for
> simulation. I have a doubt, is there any specific parameters for dimer
> simulation or we have to use similar parameters like monomer protein
> simulation. I read some literature's on dimer simulation but they are
> using similar parameters like monomer.
> --
> Regards
> Sanjay Kumar Upadhyay
> Research Scholor
> Protein Dynamics lab
> Dept of Chemistry
> IIT Powai, Mumbai, 400076
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RE: [gmx-users] mpi run

[#ZHAO LINA#]

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 your problems, just cause I once confused about 
why mine 4cpus barely used before too.

Best,

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Carsten Kutzner [ckut...@gwdg.de]
Sent: Thursday, July 08, 2010 4:04 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] mpi run

Hi Mahmoud,

for anyone to be able to help you, you need to provide
a lot more information, at least:
- which mpi library are you using?
- how did you compile and/or install Gromacs?
- what commands do you use to run mdrun and what was
the output of it?

Best,
  Carsten


On Jul 8, 2010, at 9:41 AM, nanogroup wrote:

Dear GMX Users,

I have a PC with 4 CPU, but the Gromacs only use one CPU.

the command of mpiru works on linux; however, the command of mdrun_mpi does not 
work.

Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4

Many thanks,
Mahmoud



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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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RE: [gmx-users] Energy minimisation of solvated protein - Tutorial

[#ZHAO LINA#]

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 users
Subject: Re: [gmx-users] Energy minimisation of solvated protein - Tutorial

Hi Nayef,

Can you

- copy-paste the sequence of commands as you have typed them in (not
as you think you typed them in or as they're given in the tutorial)
- provide the output of 'tail 1qlz-water.gro'

Cheers,

Tsjerk

On Mon, Jun 21, 2010 at 9:49 PM, Nayef Daher  wrote:
> Hi,
>
> I have the same problem as listed below back in February. I am using the
> latest gromacs version (4.0.7) and tried the solution below by entering
>
> genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro
>
> instead of making the output as pdb file. Yet the same result occurs with
> the same error message. One of the box lengths is smaller than twice the
> cut-off length.
>
> Please let me know what other options I can try.
>
> Thanks!
>
> nayef
> --
> original message below
> --
>
> Hi Anna,
>
> You should mention the version of Gromacs you're using. One of the
> versions did not write the box correctly to pdb files, which I think
> happened in your case. If you take as the solvation step
>
> genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro
>
> instead of writing output to 1qlz-water.pdb, I think you should be fine.
>
> The reason for writing a .pdb file is the easier visualization with a
> multitude of programs.
>
> Thanks for your interest in the tutorial.
>
> Cheers,
>
> Tsjerk
>
> On Fri, Feb 26, 2010 at 1:27 PM, Anna Duncan
>  wrote:
>>
>> Hi,
>>
>> I've been trying to go through the 'Introduction to Molecular Dynamics
>> Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of the
>> tutorials listed on the GROMACS website.
>>
>> I've got to the stage where I am performing energy minimisation on my
>> solvated protein but when I use grompp to create the .tpr file for mdrun,
>> I
>> get the error message:
>>
>> One of the box lengths is smaller than twice the cut-off length. Increase
>> the box size or decrease rlist
>>
>>
>> I am using the protein with pdb ID 1QLZ, one of the suggested structures
>> for
>> the tutorial and have so far carried out the following commands:
>>
>> % pdb2gmx -f 1qlz.pdb -o 1qlz.gro -p 1qlz.top -ignh
>> % grompp -f minim.mdp -c 1qlz.gro -p 1qlz.top -o 1qlz-EM-vacuum.tpr
>> % mdrun -v -deffnm 1qlz-EM-vacuum.tpr -c 1qlz-EM-vacuum.pdb
>> % editconf -f 1qlz-EM-vacuum.pdb -o 1qlz-PBC.gro -bt dodecahedron -d 1.0
>> % genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.pdb
>> % grompp -v -f minim.mdp -c 1qlz-water.pdb -p 1qlz.top -o 1qlz-water.tpr
>> % genion -s 1qlz-water.tpr -o 1qlz-solvated.pdb -conc 0.15 -neutral -pname
>> NA+ -nname CL-
>> % grompp -v -f minim_pbc.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o
>> 1qlz-EM-solvated.tpr
>>
>> after which I receive the error message.
>>
>> The minim_pbd.mdp file I use in the last grompp command is the same as
>> minim.mdp used in previous grompp commands (the latter file I downloaded
>> as
>> part of the tutorial) except that the line 'pbc = no' has been replaced by
>> 'pbc = xyz'.
>>
>> I have tried increasing the value of 'd' in the editconf command, to 2,3
>> and
>> even 8 but this doesn't make any difference.  (I have read that it is not
>> a
>> good idea to tamper with the cut-off values so have avoided doing that)
>>  The
>> box vector lengths when d = 1.0 are all 7.10051, and rvdw, rcoulomb = 1.0
>> in
>> mimim.mdp and minim_pbd.mdp, so I don't understand what is going wrong...
>>
>> Anna
>> --
>> gmx-users mailing listgmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
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>> or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
--
gmx-users mailing listg

RE: [gmx-users] No default Proper Dih. types

[#ZHAO LINA#]

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, June 19, 2010 8:54 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] No default Proper Dih. types

fancy2012 wrote:
> Dear GMX users,
>
> When I run grompp, I got this error " No default Proper Dih. types", how
> should I figure it out? Thanks in advance!
>

Whatever force field you're trying to use does not have a dihedral term for that
type of dihedral.  Either obtain suitable parameters from the literature,
parameterize it yourself, or use a different force field that can accommodate
this term.

-Justin

> All the best,
> fancy
>

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] the box lengths

[#ZHAO LINA#]

Thanks all, I know what's wrong now.

I forgot to set pbc = xyz earlier.

By the way,  is it normal for test failure of the gmxtest?  such as 
:~/src/gmxtest$ ./gmxtest.pl complex
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in water
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: [gmx-users] the box lengths

Well...

There is one line in try2-water.pdb, shows as below

TITLE Protein
REMARKTHIS IS A SIMULATION BOX
CRYST1   86.185   86.185   86.185  60.00  60.00  90.00 P 1   1

Do you think something was wrong during
genion -s try2-water.tpr -o try2-water-ions.pdb -conc 0.15 -neutral -pname NA+ 
-nname CL-

Thanks,

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 1:41 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths

Well, there's ya problem :-)

That specifies the box dimensions.

Have a look at try2-water.pdb as well, then you should be able to pin
down where the issue has arisen.  Appears that one of those steps have
failed to write the box dimensions.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.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: Tuesday, 15 June 2010 3:37 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
>
> 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
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
>
> What is the contents of the CRYST1 line in the file try2-water-
> ions.pdb?
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.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.
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
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RE: [gmx-users] the box lengths

[#ZHAO LINA#]

Well...

There is one line in try2-water.pdb, shows as below

TITLE Protein
REMARKTHIS IS A SIMULATION BOX
CRYST1   86.185   86.185   86.185  60.00  60.00  90.00 P 1   1

Do you think something was wrong during
genion -s try2-water.tpr -o try2-water-ions.pdb -conc 0.15 -neutral -pname NA+ 
-nname CL-

Thanks,

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 1:41 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths

Well, there's ya problem :-)

That specifies the box dimensions.

Have a look at try2-water.pdb as well, then you should be able to pin
down where the issue has arisen.  Appears that one of those steps have
failed to write the box dimensions.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.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: Tuesday, 15 June 2010 3:37 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
>
> 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
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
>
> What is the contents of the CRYST1 line in the file try2-water-
> ions.pdb?
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.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.
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
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RE: [gmx-users] the box lengths

[#ZHAO LINA#]

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
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths

What is the contents of the CRYST1 line in the file try2-water-ions.pdb?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.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.
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RE: [gmx-users] the box lengths

[#ZHAO LINA#]

(single precision)
Using a coulomb cut-off of 1 nm
Will try to add 43 NA+ ions and 41 CL- ions.

///

After vim the topol.top and the minim.mdp which pbc=no to pbc=xyz,

grompp -f minim.mdp -c try2-water-ions.pdb -p topol.top -o 
try2-EM-water-ions.tpr


double-checking input for internal consistency...
ERROR: One of the box lengths is smaller than twice the cut-off length. 
Increase the box size or decrease rlist.

///

but if I still used the pbc=no, it will work fine at this steps. 

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 11:15 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths

As already mentioned by Justin, unless you copy and paste the commands
and output you got, for us to see, we can only have stabs in the dark
(which is what I did since you are missing lots of information on what
you are actually doing) to what is actually going on.  And don't type in
the commands into your email client, physically go and copy and paste
the text in, otherwise you are filtering it through your own mind.

Go and run the series of commands that work, copy / paste the results
for us to see.

Then go and run the series of commands that don't work, copy / paste
again.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.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: 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. So
> it's not the reason about the commands I used.
>
> It did not contain the same number of molecules after genion when I
> changed the box size. The pressure coupling was not on, and I did not
> reach this steps. The problem I had just the steps I did the energy
> minimization after ions (NA+ and CL-) added.
>
> 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 6:48 AM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
>
> Please copy and paste in the commands you are using, and the output.
>
> I suspect you have made your box bigger, but it still contains the
same
> number of molecules and you still have pressure coupling on. So when
> you
> start the simulation, not surprising that the box compresses again and
> goes under 2nm again.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.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: Tuesday, 15 June 2010 12:04 AM
> > To: jalem...@vt.edu; Discussion list for GROMACS users
> > Subject: RE: [gmx-users] the box lengths
> >
> >
> > 
> > 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# wrote:
> > > ___
> > > 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
> > > Subje

RE: [gmx-users] the box lengths

[#ZHAO LINA#]

I used the same commands trying another proteins, but no problems. So it's not 
the reason about the commands I used.

It did not contain the same number of molecules after genion when I changed the 
box size. The pressure coupling was not on, and I did not reach this steps. The 
problem I had just the steps I did the energy minimization after ions (NA+ and 
CL-) added. 

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 6:48 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths

Please copy and paste in the commands you are using, and the output.

I suspect you have made your box bigger, but it still contains the same
number of molecules and you still have pressure coupling on. So when you
start the simulation, not surprising that the box compresses again and
goes under 2nm again.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.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: Tuesday, 15 June 2010 12:04 AM
> To: jalem...@vt.edu; Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
>
>
> 
> 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# wrote:
> > ___
> > 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 the testing consideration, but still has the same problem.
> >>
> >
> > Well, what are your box vectors?  If they are < 2 nm, you will get
> this error
> > because of the minimum image convention.
> >
> >
>
http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Conventi
> on
> >
> > -Justin
> >
> > system size :  4.581  2.380  2.715 (nm)
> > diameter:  4.889   (nm)
> > center  : -0.012  0.003 -0.904 (nm)
> > box vectors :  0.000  0.000  0.000 (nm)
> > box angles  :   0.00   0.00   0.00 (degrees)
> > box volume  :   0.00   (nm^3)
> > shift   :  9.678  9.664  5.461 (nm)
> > new center  :  9.667  9.667  4.557 (nm)
> > new box vectors : 12.889 12.889 12.889 (nm)
> > new box angles  :  60.00  60.00  90.00 (degrees)
> > new box volume  :1514.05   (nm^3)
> >
> > This one I set was really large, but still showed that problems.
> >
>
> What problems?  The same error about the box lengths being shorter
than
> twice
> the cutoff?  I don't think that's possible, given those vectors, if
> you're
> keeping your cutoffs at 1.0 nm.
>
> -Justin
>
> I do keep the cut-off. That's I do not know why. Four times had been
> tried.
>
> > Thanks,
> >
> > lina
> >
> >
> >
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post

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 10:02 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] the box lengths

#ZHAO LINA# wrote:
> ___
> 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 the testing consideration, but still has the same problem.
>>
>
> Well, what are your box vectors?  If they are < 2 nm, you will get this error
> because of the minimum image convention.
>
> http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention
>
> -Justin
>
> system size :  4.581  2.380  2.715 (nm)
> diameter:  4.889   (nm)
> center  : -0.012  0.003 -0.904 (nm)
> box vectors :  0.000  0.000  0.000 (nm)
> box angles  :   0.00   0.00   0.00 (degrees)
> box volume  :   0.00   (nm^3)
> shift   :  9.678  9.664  5.461 (nm)
> new center  :  9.667  9.667  4.557 (nm)
> new box vectors : 12.889 12.889 12.889 (nm)
> new box angles  :  60.00  60.00  90.00 (degrees)
> new box volume  :1514.05   (nm^3)
>
> This one I set was really large, but still showed that problems.
>

What problems?  The same error about the box lengths being shorter than twice
the cutoff?  I don't think that's possible, given those vectors, if you're
keeping your cutoffs at 1.0 nm.

-Justin

I do keep the cut-off. That's I do not know why. Four times had been tried. 

> Thanks,
>
> lina
>
>
>

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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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 the testing consideration, but still has the same problem.
>

Well, what are your box vectors?  If they are < 2 nm, you will get this error
because of the minimum image convention.

http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention

-Justin

system size :  4.581  2.380  2.715 (nm)
diameter:  4.889   (nm)
center  : -0.012  0.003 -0.904 (nm)
box vectors :  0.000  0.000  0.000 (nm)
box angles  :   0.00   0.00   0.00 (degrees)
box volume  :   0.00   (nm^3)
shift   :  9.678  9.664  5.461 (nm)
new center  :  9.667  9.667  4.557 (nm)
new box vectors : 12.889 12.889 12.889 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  :1514.05   (nm^3)

This one I set was really large, but still showed that problems.

Thanks,

lina


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[gmx-users] the box lengths

[#ZHAO LINA#]

 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 the testing 
consideration, but still has the same problem.

integrator  = steep
emtol   = 1.0
nsteps  = 500
nstenergy   = 1
energygrps  = System

ns_type = simple
coulombtype = cut-off
rcoulomb= 1.0
rvdw= 1.0
constraints = none
pbc = xyz

Thanks for any advice,

Best regards,

lina

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RE: [gmx-users] velocity autocorrelation function.

[#ZHAO LINA#]

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) which computes the velocity autocorrelation function, 
> it's really hard for me to read such a nice codes.
> If I want to know much more about the specific formula of velocity 
> autocorrelation functions which is being used in gromacs and how it's 
> implemented, which way I should go?
>
> Great appreciation for any advice,
>
> Best Regards,
>
> lina
This is described quite well in the textbook by Allen adn Tildesley
(1987) you will find the reference in the manual.


Thanks, I am reading this ebook now. Just wonder there are some latest ones. 

Best Regards,

lina
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] velocity autocorrelation function.

[#ZHAO LINA#]

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 to read such a nice codes.
If I want to know much more about the specific formula of velocity 
autocorrelation functions which is being used in gromacs and how it's 
implemented, which way I should go?

Great appreciation for any advice,

Best Regards,

lina
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[gmx-users] xml

[#ZHAO LINA#]

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

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[gmx-users] Re: Re: loab imbalance

[#ZHAO 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 load imbalance: 1500.0 %
> >>>   Part of the total run time spent waiting due to load imbalance:
> 187.5 %
> >>>   Steps where the load balancing was limited by -rdd, -rcon and/or
> -dds:
> >>> X 0 % Y 0 %
> >>>
> >>> NOTE: 187.5 % performance was lost due to load imbalance
> >>>in the domain decomposition.
> >> You ran an inefficient but otherwise valid computation. Check out
> the 
> >> manual section on domain decomposition to learn why it was
> inefficient, 
> >> and whether you can do better.
> >>
> >> Mark
> > 
> > I search the "decomposition" keyword on Gromacs manual, no match
> found.
> > Are you positive about that? Thanks any way, but can you make it more
> 
> The title of section 3.17 is "Domain Decomposition" and discusses the
> algorithm 
> and mdrun parameters relevant to controlling performance.
> 
> -Justin
> 
> Sorry, the acroread is really not sensitive in searching "domain" or
> "decomposition" on version 3.3. I did the same search on version 3.2 and
> I found it. I am not so familiar with this manual. Thanks again.
> 
> lina 

Since you performance roughly doubles when going from 8 to 16 cores,
I think there is no significant load imbalance and there is a bug in the routine
that calculates the total load imbalance.

In my previous mail I asked which Gromacs version you are using.
Could you please tell me this?

Berk


Hi, it's version 4.0.7. Sorry, mainly I will consider using the latest (better 
stable) version, so last time I forgot to answer you.
I also run it on cluster before, it does not have such problems (by my careless 
mistakes, I overwrite it when I tried to compare the results from the 
multicores, and it's days ago and I barely could not remember exactly, I 
worried I might ignore the problems, so I re-run it again, and the results will 
wait for a while). Thanks for those suggestions they gave for me to read the 
manuals. 
The machine I used is single multicore machine with 64 bits kernel.

Thanks and regards,

lina



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[gmx-users] Re: Hessian Matrix

[#ZHAO LINA#]

Hi,

I just simply did a change in .mdp file. Now the integrator = nm
after grompp, 

1) below is the error of  mdrun -s em.tpr -mtx em.mtx

Program mdrun, VERSION 4.0.7
Source code file: ../../../../src/gmxlib/smalloc.c, line: 147

Fatal error:
Not enough memory. Failed to calloc 4118944041 elements of size 4 for 
full_matrix
(called from file ../../../../src/mdlib/minimize.c, line 2219)

2) Seems the one run in cluster choked there like this in md.log.
Linking all bonded interactions to atoms
There are 2106 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME

The initial number of communication pulses is: X 1 Y 1
The initial domain decomposition cell size is: X 2.76 nm Y 1.07 nm

The maximum allowed distance for charge groups involved in interactions is:
 non-bonded interactions   1.000 nm
two-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.
> 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)
> ## program to run
> mpirun -np $NCPUS mdrun_mpi -s em.tpr -mtx em.mtx 
> 

Probably because the Hessian is only relevant when doing normal mode 
calculations (or perhaps L-BFGS minimization).  I suspect that if you're not 
using the nm integrator, then you're not going to get the Hessian.

-Justin

> Thanks and best,
> 
> lina
> 

-- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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[gmx-users] Hessian Matrix

[#ZHAO LINA#]

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)
## program to run
mpirun -np $NCPUS mdrun_mpi -s em.tpr -mtx em.mtx 

Thanks and best,

lina
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[gmx-users] Re:mpi_run issue

[#ZHAO LINA#]

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 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=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS

## program to run
/usr/local/openmpi/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE ./myprog 


My working directory is ${HOME}/Jobs/1A7W/tryScript. By the way, I do not know 
the NODEFILE mean.

Thanks and best regards,

Elsa

--


> 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.

We can't know the best procedure for your cluster because we haven't read its 
documentation or talked to its admins... (hint, hint)

> Thanks and best regards,
> 
> Elsa
> 
> #!/bin/bash
> #
> ## Specify the job name
> #PBS -N emMDrunSecondOne
> 
> ## 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
> 
> PBS_O_WORKDIR=${HOME}/Jobs/1A7W/tryScript
> [ -d ${PBS_O_WORKDIR}] || exit 1

This looks wrong. PBS usually has flags that let you specify running the job in 
directory from which submission occured - use them.
 
> cd $PBS_O_WORKDIR
> NCPUS=`cat $PBS_NODEFILE | wc -l`
> echo $NCPUS

If PBS is defining $PBS_NODEFILE to point to some file it creates, then that 
file won't be local to the directory you've arbitrarily changed to, so NCPUS 
won't get defined suitably, so mpirun won't work.

I'd suggest you start again from some example script that is known to work on 
your cluster and modify only the mpirun line.

Mark

> ## program to run
> /usr/local/openmpi/bin/mpirun -np $NCPUS mdrun_mpi -deffnm em 
> exit 0
> > -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search 
> before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


--

Message: 2
Date: Thu, 28 Jan 2010 16:03:50 +0100
From: Erik Marklund 
Subject: Re: [gmx-users] hblife
To: Discussion list for GROMACS users 
Message-ID: <4b61a756.7060...@xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

afsaneh maleki skrev:
> thanks dear justin'
>
> it is right that the output of the analysis tools generally writes 
> axis labels and data set legends. in hblife.xyg  file is written that  
> x axis  label "Time (ps)" and the last time is written 14300.001 
> whereas my simulated time is 4 ps not 143000.00 ps   
> i send you this file
I don't remember the details about the calculation of lifetimes, but I 
believe it's an estimate of how the half lifes of hydrogen bonds. You 
can also get this quantity, along with the kinetic constants and 
energies for hb breaking and frormation, using -ac. If I remember 
correctly, -ac uses a more reliable method.

Erik
>
> Best wishes,
> Afsaneh
>
> On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul  > wrote:
>
>
>
> afsaneh maleki wrote:
>
> Hi,
>
> would you please elaborate the first column in the  hblife.xvg
> file?
> hblife.xyg is the output of the following command:
> g_hbond -life hblife.xvg
> this column don't show the real time in simulated system.what
> are these times?
>
>
> Check the headers in the .xvg file; the output of the analysis
> tools generally writes axis labels and data set legends.  If it
> still doesn't make sense, post a snippet of your file.
>
> -Justin
>
> thanks in advance,
> Afsaneh
>
>
> -- 
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu  | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> 
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or sen

[gmx-users] RE: gmx-users Digest, Vol 69, Issue 145

[#ZHAO LINA#]

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=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS

## program to run
/usr/local/openmpi/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE ./myprog 


My working directory is ${HOME}/Jobs/1A7W/tryScript. By the way, I do not know 
the NODEFILE mean.

Thanks and best regards,

Elsa

--


> 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.

We can't know the best procedure for your cluster because we haven't read its 
documentation or talked to its admins... (hint, hint)

> Thanks and best regards,
> 
> Elsa
> 
> #!/bin/bash
> #
> ## Specify the job name
> #PBS -N emMDrunSecondOne
> 
> ## 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
> 
> PBS_O_WORKDIR=${HOME}/Jobs/1A7W/tryScript
> [ -d ${PBS_O_WORKDIR}] || exit 1

This looks wrong. PBS usually has flags that let you specify running the job in 
directory from which submission occured - use them.
 
> cd $PBS_O_WORKDIR
> NCPUS=`cat $PBS_NODEFILE | wc -l`
> echo $NCPUS

If PBS is defining $PBS_NODEFILE to point to some file it creates, then that 
file won't be local to the directory you've arbitrarily changed to, so NCPUS 
won't get defined suitably, so mpirun won't work.

I'd suggest you start again from some example script that is known to work on 
your cluster and modify only the mpirun line.

Mark

> ## program to run
> /usr/local/openmpi/bin/mpirun -np $NCPUS mdrun_mpi -deffnm em 
> exit 0
> > -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search 
> before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


--

Message: 2
Date: Thu, 28 Jan 2010 16:03:50 +0100
From: Erik Marklund 
Subject: Re: [gmx-users] hblife
To: Discussion list for GROMACS users 
Message-ID: <4b61a756.7060...@xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

afsaneh maleki skrev:
> thanks dear justin'
>
> it is right that the output of the analysis tools generally writes 
> axis labels and data set legends. in hblife.xyg  file is written that  
> x axis  label "Time (ps)" and the last time is written 14300.001 
> whereas my simulated time is 4 ps not 143000.00 ps   
> i send you this file
I don't remember the details about the calculation of lifetimes, but I 
believe it's an estimate of how the half lifes of hydrogen bonds. You 
can also get this quantity, along with the kinetic constants and 
energies for hb breaking and frormation, using -ac. If I remember 
correctly, -ac uses a more reliable method.

Erik
>
> Best wishes,
> Afsaneh
>
> On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul  > wrote:
>
>
>
> afsaneh maleki wrote:
>
> Hi,
>
> would you please elaborate the first column in the  hblife.xvg
> file?
> hblife.xyg is the output of the following command:
> g_hbond -life hblife.xvg
> this column don't show the real time in simulated system.what
> are these times?
>
>
> Check the headers in the .xvg file; the output of the analysis
> tools generally writes axis labels and data set legends.  If it
> still doesn't make sense, post a snippet of your file.
>
> -Justin
>
> thanks in advance,
> Afsaneh
>
>
> -- 
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu  | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> 
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org
> .
> Can't post? Read http://www.gromacs.org/mailing_li

[gmx-users] mpi_run issue

[#ZHAO LINA#]

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 regards,

Elsa

#!/bin/bash
#
## Specify the job name
#PBS -N emMDrunSecondOne

## 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

PBS_O_WORKDIR=${HOME}/Jobs/1A7W/tryScript
[ -d ${PBS_O_WORKDIR}] || exit 1

cd $PBS_O_WORKDIR
NCPUS=`cat $PBS_NODEFILE | wc -l`
echo $NCPUS

## program to run
/usr/local/openmpi/bin/mpirun -np $NCPUS mdrun_mpi -deffnm em 
exit 0

<>-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
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