[gmx-users] RE: how many water molecule used to run MD?

[Vitaly Chaban]

> If I want to include more than 1000 TIP4P or TIP5P water molecules in
> my MD system, how could I construct the TIP4P.gro and TIP5P.gro files
> ?

genconf -f onewater.gro -o box.gro -nbox N N N,

where onewater.gro contains the coordinates of one water molecule and
N - is a number of water molecules per cubic box side.

genbox -cp onewater.gro -cs onewater.gro -o box.gro -box N N N -maxsol
M,

where M is a desired number of molecules in the box, N - is each side
length in nanometers.


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +38-097-8259698

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[gmx-users] RE: how many water molecule used to run MD?

[Vitaly Chaban]

> Hi
> how many water molecules used to run MD?
> 
> what is the criteria for this?

So many to make your short-range potential saturated.


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +38-097-8259698

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[gmx-users] RE: TIP4P and TIP5P

[Vitaly Chaban]

> Could anyone tell me how to construct the solvent box of  TIP4P and TIP5P 
> model?

First of all you should make the coordinates of one particle of the
desired model in .gro file format. For the next commands see my previous 
messages.

Cheers.


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +38-097-8259698

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[gmx-users] Re: how many water molecule used to run MD?

[Chih-Ying Lin]

Hi
Would you please explain "the short-range potential saturated"?

What is the short-range potential?
Also, how to measure the short-range potential?

Thank you
Lin

On 9/22/08, Vitaly Chaban <[EMAIL PROTECTED]> wrote:
> > Hi
>  > how many water molecules used to run MD?
>  >
>  > what is the criteria for this?
>
>
> So many to make your short-range potential saturated.
>
>
>
>  --
>  Vitaly V. Chaban
>  School of Chemistry
>  National University of Kharkiv
>  Svoboda sq.,4, Kharkiv 61077, Ukraine
>  email: [EMAIL PROTECTED]
>  skype: vvchaban
>  tel.: +38-097-8259698
>
>
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[gmx-users] Atom type: N inside the R-N(CH3)3

[Chih-Ying Lin]

Hi
What is the atom type of Nitrogen inside the molecule  R-N(CH3)3  ?

I check the ffG53a5.itp and ffG53a6.itp and the related Gromos FF papers.

There are 6 atom types for Nitrogen.
N peptide nitrogen (NH)
NT   terminal nitrogen (NH2)
NL   terminal nitrogen  (NH3)
NR  aromatic nitrogen
NZ  Arg NH (NH2)
NE  Arg NE (NH)

My understanding is either NT or NL but not sure which is the exact one.

Thank you
Lin
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RE: [gmx-users] PME 3dc geometry and the optimal PME mesh load

[Berk Hess]

Yes.

The manual and also mdp options of the jsut released 4.0 version
will tell you that you can increase your cut-off and PME grid spacing by the 
same factor
to lower the PME load.

Berk



Date: Sun, 21 Sep 2008 23:24:13 +0800
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] PME 3dc geometry and the optimal PME mesh load

Hi all,
 
I use 3dc geometry for a system with large box size in z direction, and when I 
try the new CVS version, I find a note saying "The optimal PME mesh load is 
usually between 025 and 0.33, you should probably increase the cut-off and the 
PME grid spacing". A quite large estimation 0.86 was reported in grompp, and I 
wonder if I can do sth to speed up the simulation. Thanks for your suggestions 
in advance.

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[gmx-users] Re[2]: how many water molecule used to run MD?

[Vitaly Chaban]

CYL> Would you please explain "the short-range potential saturated"?

Usually it is the same as Lennard-Jones potential. The each side of
your box must be two times larger (see also about cut-off) than the
distance where the value of the short-range potential is (very close to) zero.

In fluids, this value is from 1.0 nm to 1.4 nm, for water it's even less.
See force field specifications for the exact models you use.


CYL> What is the short-range potential?
CYL> Also, how to measure the short-range potential?

CYL> Thank you
CYL> Lin

CYL> On 9/22/08, Vitaly Chaban <[EMAIL PROTECTED]> wrote:
>> > Hi
>>  > how many water molecules used to run MD?
>>  >
>>  > what is the criteria for this?
>>
>>
>> So many to make your short-range potential saturated.
>>




-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +38-097-8259698

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Re: [gmx-users] Leaflet of Bilayer

[Alan Dodd]

(Yes, what Chris Neale said).  I had to do something similar myself, to make a 
256-lipid square box from a 128 lipid box.  I used genbox to make a new, larger 
square box using my original lipid patch as the input file, and then tinkered 
with the dimensions to get the lipids/leaflet as close to what I wanted as 
possible, then deleted the excess 1 or 2 lipids in one leaflet.  I wrote a 
small script to count the lipids in each leaflet, it's not hard to code and I 
found it immensely useful for generating leaflet-specific index files later.  I 
must admit, I only actually equilibrated it for 20ns or so.



- Original Message 
From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Monday, September 22, 2008 6:55:37 AM
Subject: [gmx-users] Leaflet of Bilayer

In my opinion, use any technique that you want (genbox included) then  
run the resulting system for >=50ns while plotting the area per lipid  
and order parameters over time. When these values stop drifting over  
time then you have an equilibrated bilayer. If you have access to a  
cluster that scales well to 4 cores then this should not take longer  
than a month. With systems that scale well to 10 cores I can  
equilibrate such a system in under two weeks. Of course, the more  
limited your resources are then the more thought that you need to put  
into your setup. Very generally, for beginners with at least moderate  
computational resources, I suggest immediately following your first  
good idea to get the system prepared and then, while it is running,  
starting to think about how it could have been done in a better way.  
With cpu resources as they are now, your initial run is likely to be  
finished faster than anything else if you start it immediately and the  
next time you go about this it will be faster because you will figure  
out the better method.

Bottom line: an equilibrated bilayer is an equilibrated bilayer, and I  
as a reader am not going to have any problem with your final results  
even if I think that you could have obtained an equilibrated bilayer  
with a quicker method.

Important note: Please use a new subject for a new topic. I know that  
topics often diverge, but you started this thread with a vmd-list  
question and now you are on to something that is only related to that  
by the fact that you study membranes.

Chris.

--- original message ---

Thanks for the response
Just diverting this topic to about specific number of popc molecules.

I created the bilayer by using genconf command
genconf -f popc128a.pdb -o out.gro -dist 0 0 0 -nbox 2 1 1 (as I  
posted  in my previous mail) generated output file contain 128 popc  
in each leaflet of bilayer.

If you see original popc box dimensions 6.1x6.2x6.9 (means in all  
dimensions popc number almost same)but with genconf command above  
mentioned options created box values 12x6.1x6.9. I dont want that many  
popc molecules because in X-dimension too many popc molecules are  
present.

1.is there anyway to reduce those popc molecules from 128 to 80/90  
popc molecules? or
2.I wanted to create popc molecules 80 or 90 in eachleaflet is it  
possible to generate?

These are may be trivial queries
Could you give suggest me please
Thanks in advance.

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Re: [gmx-users] TIP4P and TIP5P

[Jochen Hub]

You don't have to construct that stuff. Its all in the share/gromacs/top
directory of your gromacs installation. Check the gro and the itp files
there.

Jochen


Chih-Ying Lin wrote:
> Hi
> Could anyone tell me how to construct the solvent box of  TIP4P and TIP5P 
> model?
> 
> 
> And, how to construct water_TIP4P.itp and and water_TIP5P.itp ?
> 
> Thank you very much
> Lin
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> .
> 


-- 

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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Re: [gmx-users] Cann't get the same result ?

[Jochen Hub]

xuji wrote:
> Hi all:
> 
> I run mdrun of gromacs-3.3.3 6 times of a small simulation, 
> but I cann't get the same result every time. I run the mdrun 
> program using "./mdrun -v -s md1.tpr  -o md1.trr  -c after_md1.gro  -g 
> md1.log  -e md1.edr  -x md1.xtc > md1.job 
>&& ./mdrun -v -s md1.tpr  -o md1.trr  -c after_md1.gro  -g md1.log  -e 
> md1.edr  -x md1.xtc > md1.job 
>&& ./mdrun -v -s md1.tpr  -o md1.trr  -c after_md1.gro  -g md1.log  -e 
> md1.edr  -x md1.xtc > md1.job". 
> Three simulations one time. And run two times. The 6 log files are in the 
> accessory.
> Can someone tell me why cann't I get the same result of the 6 simulations?
> Appreciate any help in advance!

Check the messages by Carsten Kutzner in this list. He replied to such
questions several times in detail.

Best, Jochen


> 
> Best wishes!
> 
> Ji Xu
> [EMAIL PROTECTED]
> 
> 2008-09-22
> 　　
> 
> 
> 
> 
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-- 

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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Re: [gmx-users] output format of gromacs utilities

[Jochen Hub]

Vitaly Chaban wrote:
> Hello,
> 
> In gromacs analysis tools, is it possible to output multiple data
> columns as several 'parallel' columns (not as pairs delimited by '&')?

I don't think so, but i once wrote a script that does the transformation
for you. Here it is.

Best, Jochen


#!/bin/bash

tmpdir=x.tmp
rm -fr $tmpdir
mkdir $tmpdir

echo Removing comments...
egrep -v '^@|^#' $1 > $tmpdir/xxx.tmp

here=`pwd`
cd $tmpdir
echo "Splitting $1 at &'s ..."
csplit -n 5 --silent xxx.tmp '/&/' '{*}'
grep '[0-9]' xx0 | awk '{print $1}' > times.tmp

rm -f yy*[0-9]
for i in xx[0-9][0-9][0-9][0-9][0-9]; do
nr=$(echo $i|tr -cd [:digit:])
if grep -q '[0-9]' $i; then
echo writing yy$nr ...
grep '[0-9]' $i | awk '{print $2}' > yy$nr
fi
done

out=${1%%.xvg}.dat
paste -d ' ' times.tmp yy[0-9][0-9][0-9][0-9][0-9] > $out
echo created ${1%%.xvg}.dat


> 
> I experience difficulties to read such (xvg) format by sigmaplot.
> 
> 


-- 

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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RE: [gmx-users] output format of gromacs utilities

[Berk Hess]

Hi,

For many tools setting the environment variable
GMX_VIEW_XVG = xmgr
will work.

Berk


> Date: Mon, 22 Sep 2008 11:05:58 +0200
> From: [EMAIL PROTECTED]
> To: [EMAIL PROTECTED]; gmx-users@gromacs.org
> Subject: Re: [gmx-users] output format of gromacs utilities
> CC: 
> 
> Vitaly Chaban wrote:
> > Hello,
> > 
> > In gromacs analysis tools, is it possible to output multiple data
> > columns as several 'parallel' columns (not as pairs delimited by '&')?
> 
> I don't think so, but i once wrote a script that does the transformation
> for you. Here it is.
> 
> Best, Jochen
> 
> 
> #!/bin/bash
> 
> tmpdir=x.tmp
> rm -fr $tmpdir
> mkdir $tmpdir
> 
> echo Removing comments...
> egrep -v '^@|^#' $1 > $tmpdir/xxx.tmp
> 
> here=`pwd`
> cd $tmpdir
> echo "Splitting $1 at &'s ..."
> csplit -n 5 --silent xxx.tmp '/&/' '{*}'
> grep '[0-9]' xx0 | awk '{print $1}' > times.tmp
> 
> rm -f yy*[0-9]
> for i in xx[0-9][0-9][0-9][0-9][0-9]; do
> nr=$(echo $i|tr -cd [:digit:])
> if grep -q '[0-9]' $i; then
> echo writing yy$nr ...
> grep '[0-9]' $i | awk '{print $2}' > yy$nr
> fi
> done
> 
> out=${1%%.xvg}.dat
> paste -d ' ' times.tmp yy[0-9][0-9][0-9][0-9][0-9] > $out
> echo created ${1%%.xvg}.dat
> 
> 
> > 
> > I experience difficulties to read such (xvg) format by sigmaplot.
> > 
> > 
> 
> 
> -- 
> 
> Dr. Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> Tel.: +49 (0)551 201-2312
> 
> ___
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[gmx-users] searching the archives

[Omer Markovitch]

Shalom,
Is it just me or there is a bug in the archives search page
http://www.gromacs.org/search ?
(error 404 - page not found)
--omer.
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Re: [gmx-users] searching the archives

[David van der Spoel]

Omer Markovitch wrote:

Shalom,
Is it just me or there is a bug in the archives search page 
http://www.gromacs.org/search ?

(error 404 - page not found)
--omer.


plz go to the main site and click search.





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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re[2]: [gmx-users] output format of gromacs utilities

[Vitaly Chaban]

Jochen,

Thank you very much! I will just try it.

Vitaly


JH> Vitaly Chaban wrote:
>> Hello,
>> 
>> In gromacs analysis tools, is it possible to output multiple data
>> columns as several 'parallel' columns (not as pairs delimited by '&')?

JH> I don't think so, but i once wrote a script that does the transformation
JH> for you. Here it is.

JH> Best, Jochen


JH> #!/bin/bash

JH> tmpdir=x.tmp
JH> rm -fr $tmpdir
JH> mkdir $tmpdir

JH> echo Removing comments...
JH> egrep -v '^@|^#' $1 > $tmpdir/xxx.tmp

JH> here=`pwd`
JH> cd $tmpdir
JH> echo "Splitting $1 at &'s ..."
JH> csplit -n 5 --silent xxx.tmp '/&/' '{*}'
JH> grep '[0-9]' xx0 | awk '{print $1}' > times.tmp

JH> rm -f yy*[0-9]
JH> for i in xx[0-9][0-9][0-9][0-9][0-9]; do
JH> nr=$(echo $i|tr -cd [:digit:])
JH> if grep -q '[0-9]' $i; then
JH> echo writing yy$nr ...
JH> grep '[0-9]' $i | awk '{print $2}' > yy$nr
JH> fi
JH> done

JH> out=${1%%.xvg}.dat
JH> paste -d ' ' times.tmp yy[0-9][0-9][0-9][0-9][0-9] > $out
JH> echo created ${1%%.xvg}.dat


>> 
>> I experience difficulties to read such (xvg) format by sigmaplot.
>> 
>> 

-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +38-097-8259698

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[gmx-users] simulation in DPPC lipid bilayer

[prasun kumar]

Dear Users

I am trying to do a simulation in lipid using DPPC12a.pdb.I have done all
the necessary changes rewuired.I am using FFGMX force field
while doing positional restarined step its giving following error:

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 125 ]

But during energy minimization step I got a message that energy minimization
converges in 18 steps but dint reach the cuttoff value you specified.

I am eager to know when a person gets this type of error

Kindly help me

Waiting for your invaluable suggestions


-- 
PRASUN (ASHOKA)
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Re: [gmx-users] simulation in DPPC lipid bilayer

[Justin A. Lemkul]

prasun kumar wrote:

Dear Users

I am trying to do a simulation in lipid using DPPC12a.pdb.I have done 
all the necessary changes rewuired.I am using FFGMX force field

while doing positional restarined step its giving following error:

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 125 ]

But during energy minimization step I got a message that energy 
minimization converges in 18 steps but dint reach the cuttoff value you 
specified.


I am eager to know when a person gets this type of error


When your system is blowing up.  A similar message just hit the list a day or so 
ago (hint: check the archives when you get errors), and I provided some search 
terms and advice there:


http://www.gromacs.org/pipermail/gmx-users/2008-September/036622.html

-Justin



Kindly help me

Waiting for your invaluable suggestions


--
PRASUN (ASHOKA)




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Justin A. Lemkul
Graduate Research Assistant
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] Re:Leaflet of Bilayer

[minnale]

  Thanks alot to Chris and Alan for given their valuable suggestions

then a small doubt about time length of bilayer simulation, that is if I 
concentrate mainly on protein but not on membrane is it require to run >=50ns 
or 20ns of POPC alone before inserting protein into it.

 Earlier I performed only popc simulation for only 5ns then plotted potential 
energy(it came negative value), average area per lipid(0.64 nm^2/sec). Later 
protein embedded into 5ns simulated popc bilayer and being run simulations. 
What I have done was wrong? 
Appreciate for your help
Thanks in advance. 


>(Yes, what Chris Neale said).  I had to do something similar myself, to make a 
>256-lipid square box from a 128 lipid box.  I used genbox to make a new, 
>larger square box using my original lipid patch as the input file, and then 
>tinkered with the dimensions to get the lipids/leaflet as close to what I 
>wanted as possible, then deleted the excess 1 or 2 lipids in one leaflet.  I 
>wrote a small script to count the lipids in each leaflet, it's not hard to 
>code and I found it immensely useful for generating leaflet-specific index 
>files later.  I must admit, I only actually equilibrated it for 20ns or so.
>
>
>
>- Original Message 
> From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]>
>To: gmx-users@gromacs.org
>Sent: Monday, September 22, 2008 6:55:37 AM
>Subject: [gmx-users] Leaflet of Bilayer
>
>In my opinion, use any technique that you want (genbox included) then
>run the resulting system for >=50ns while plotting the area per lipid
>and order parameters over time. When these values stop drifting over
>time then you have an equilibrated bilayer. If you have access to a
>cluster that scales well to 4 cores then this should not take longer
>than a month. With systems that scale well to 10 cores I can
>equilibrate such a system in under two weeks. Of course, the more
>limited your resources are then the more thought that you need to put
>into your setup. Very generally, for beginners with at least moderate
>computational resources, I suggest immediately following your first
>good idea to get the system prepared and then, while it is running,
>starting to think about how it could have been done in a better way.
>With cpu resources as they are now, your initial run is likely to be
>finished faster than anything else if you start it immediately and the
>next time you go about this it will be faster because you will figure
>out the better method.
>
>Bottom line: an equilibrated bilayer is an equilibrated bilayer, and I
>as a reader am not going to have any problem with your final results
>even if I think that you could have obtained an equilibrated bilayer
>with a quicker method.
>
>Important note: Please use a new subject for a new topic. I know that
>topics often diverge, but you started this thread with a vmd-list
>question and now you are on to something that is only related to that
>by the fact that you study membranes.
>
>Chris.
>
>--- original message ---
>
>Thanks for the response
>Just diverting this topic to about specific number of popc molecules.
>
>I created the bilayer by using genconf command
>genconf -f popc128a.pdb -o out.gro -dist 0 0 0 -nbox 2 1 1 (as I
>posted  in my previous mail) generated output file contain 128 popc
>in each leaflet of bilayer.
>
>If you see original popc box dimensions 6.1x6.2x6.9 (means in all
>dimensions popc number almost same)but with genconf command above
>mentioned options created box values 12x6.1x6.9. I dont want that many
>popc molecules because in X-dimension too many popc molecules are
>present.
>
>1.is there anyway to reduce those popc molecules from 128 to 80/90
>popc molecules? or
>2.I wanted to create popc molecules 80 or 90 in eachleaflet is it
>possible to generate?

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[gmx-users] Polystyrene box

[Andrea Muntean]

Hello,

we are trying to generate a polystyrene box. We have a homemade pdb file,
but the residues are not recognised. Have somebody a good pdb file or can
tell me what are the standard residues in Gromax?
Any other good hints are welcome.

Thanks a lot,
Andrea
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[gmx-users] MD for two merged chains

[DimitryASuplatov]

Hello,
I have a two-chain protein. I want to merge N-terminal residue of chain
A with C-terminal of chain B. I can tweak the coordinates with pymol but
when I run energy minimization two chains split again because gromacs
fairly treats the input as a two-chain protein. 
I could switch the ATOM entries for chains A and B in the coordinate
file - so that they are in the right order - and then delete the chain
identifier, this workout will not help in more complex situations like 4
chains merge though.
Is there any option that allows gromacs not to consider chain IDs and
the order of aa in the coordinate?
Thanks. I really appreciate your help.
SDA

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Re: [gmx-users] Announcing: Gromacs 4.0, release candidate 1

[Sagittarius]

What compiler should I use on Windows?
Thank you in advance.

--- On Sun, 9/21/08, Erik Lindahl <[EMAIL PROTECTED]> wrote:

From: Erik Lindahl <[EMAIL PROTECTED]>
Subject: [gmx-users] Announcing: Gromacs 4.0, release candidate 1
To: "Discussion list for GROMACS users" 
Date: Sunday, September 21, 2008, 11:46 PM

Stockholm, September 22 2008


In a bold move today, the Gromacs developers finally decided not to  
wait for Duke Nukem Forever before releasing Gromacs 4.0, and just put  
out release candidate 1 together with a new manual at

ftp://ftp.gromacs.org:/pub/beta/

"We realize it could be a big disappointment to many users not having  
g_dukenukemforever built-in, but sometimes you have to make hard  
decisions. Had we waited further, we might even have had to release  
Gromacs 5 before Gromacs 4", an anonymous developer said.


If you haven't already been playing around with CVS for the last year  
we think you'll be pretty impressed with the scalability of the new  
code, in addition to full checkpointing support, REMD, and various  
optimizations.

Having said that, since the code has changed a lot we decided to have  
a fairly short cycle of "release candidates" before putting out the  
real version. Please download the code above, try to compile and run  
with it (see manual and html pages in the distro for documentation of  
new stuff), and submit any bugs you find to bugzilla ("If it's not in 

bugzilla, it's not a bug").


Have fun!

Erik, Berk, and David.


  
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Re: [gmx-users] Announcing: Gromacs 4.0, release candidate 1

[Erik Lindahl]

Hi,

One extra comment: By default, checkpointing will result in separate  
output files to avoid filling up your disk,  or just in case something  
horrible happens just when we are about to resume the simulation.  
There are also some old strange versions of the GPFS file system where  
append operations are not allowed (no idea what happens if we were to  
try it anyway).



However...  it IS possible to have Gromacs 4 automatically checkpoint  
and just append to the previous output files if you (think you) know  
what you're doing. We haven't experienced any bugs with this yet, but  
this is one of the things we'd like you to test!


So, to enable all this stuff, simply execute mdrun e.g. as:

mdrun -v -deffnm test -cpi test -append


* The -cpi option will tell mdrun to look for the checkpoint file (the  
first time when we don't have it, you'll just get a normal run)
* The -append option will tell mdrun to append to the previous output  
files.


Thus: the command line should preferrably be identical in all runs.  
This far we've only tested it when we're nice and don't move files,  
but feel free to stress-test it and report bugs to us. Don't complain  
if your trajectories are eaten after you've moved them in the middle  
of a simulation, though ;-)


Cheers,

Erik




On Sep 22, 2008, at 8:46 AM, Erik Lindahl wrote:


Stockholm, September 22 2008


In a bold move today, the Gromacs developers finally decided not to  
wait for Duke Nukem Forever before releasing Gromacs 4.0, and just  
put out release candidate 1 together with a new manual at


ftp://ftp.gromacs.org:/pub/beta/

"We realize it could be a big disappointment to many users not  
having g_dukenukemforever built-in, but sometimes you have to make  
hard decisions. Had we waited further, we might even have had to  
release Gromacs 5 before Gromacs 4", an anonymous developer said.



If you haven't already been playing around with CVS for the last  
year we think you'll be pretty impressed with the scalability of the  
new code, in addition to full checkpointing support, REMD, and  
various optimizations.


Having said that, since the code has changed a lot we decided to  
have a fairly short cycle of "release candidates" before putting out  
the real version. Please download the code above, try to compile and  
run with it (see manual and html pages in the distro for  
documentation of new stuff), and submit any bugs you find to  
bugzilla ("If it's not in bugzilla, it's not a bug").



Have fun!

Erik, Berk, and David.


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Associate Professor, Computational Structural Biology
Center for Biomembrane Research, Dept. Biochemistry & Biophysics
Stockholm University, SE-106 91 Stockholm, Sweden
Tel: +46(0)8164675  Mobile: +46(0)703844534  Fax: mail a PDF instead






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Re: [gmx-users] Announcing: Gromacs 4.0, release candidate 1

[Erik Lindahl]

MSVC should be able to compile it, but you'll have to create the  
makefiles/build environment yourself.


Alternatively, the easy route is to install cygwin (or get a mac ;-)

Cheers,

Erik

On Sep 22, 2008, at 4:36 PM, Sagittarius wrote:


What compiler should I use on Windows?
Thank you in advance.

--- On Sun, 9/21/08, Erik Lindahl <[EMAIL PROTECTED]> wrote:
From: Erik Lindahl <[EMAIL PROTECTED]>
Subject: [gmx-users] Announcing: Gromacs 4.0, release candidate 1
To: "Discussion list for GROMACS users" 
Date: Sunday, September 21, 2008, 11:46 PM

Stockholm, September 22 2008


In a bold move today, the Gromacs developers finally decided not to
wait for Duke Nukem Forever before releasing Gromacs 4.0, and just put
out release candidate 1 together with a new manual at

ftp://ftp.gromacs.org:/pub/beta/

"We realize it could be a big disappointment to many users not having
g_dukenukemforever built-in, but sometimes you have to make hard
decisions. Had we waited further, we might even have had to release
Gromacs 5 before Gromacs 4", an anonymous developer said.


If you haven't already been playing around with CVS for the last year
we think you'll be pretty impressed with the scalability of the new
code, in addition to full checkpointing support, REMD, and various
optimizations.

Having said that, since the code has changed a lot we decided to have
a fairly short cycle of "release candidates" before putting out the
real version. Please download the code above, try to compile and run
with it (see manual and html pages in the distro for documentation of
new stuff), and submit any bugs you find to bugzilla ("If it's not in

bugzilla, it's not a bug").


Have fun!

Erik, Berk, and David.



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Erik Lindahl   <[EMAIL PROTECTED]>  Backup: <[EMAIL PROTECTED]>
Associate Professor, Computational Structural Biology
Center for Biomembrane Research, Dept. Biochemistry & Biophysics
Stockholm University, SE-106 91 Stockholm, Sweden
Tel: +46(0)8164675  Mobile: +46(0)703844534  Fax: mail a PDF instead






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Re: [gmx-users] Polystyrene box

[Justin A. Lemkul]

Andrea Muntean wrote:

Hello,
 
we are trying to generate a polystyrene box. We have a homemade pdb 
file, but the residues are not recognised. Have somebody a good pdb file 
or can tell me what are the standard residues in Gromax?

Any other good hints are welcome.


Residues that are recognized by the standard force fields are stored in .rtp 
files.  You will likely have to create an entry in the appropriate .rtp for a 
styrene monomer.  I believe I have seen posts to this list about such topics, so 
check the archives for the questions that were asked and the responses that were 
given.


-Justin

 
Thanks a lot,

Andrea




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--


Justin A. Lemkul
Graduate Research Assistant
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] Search more information of Atom type: N inside the R-N(CH3)3

[Chih-Ying Lin]

Hi
What is the atom type of Nitrogen inside the molecule  R-N(CH3)3  ?

I check the ffG53a5.itp and ffG53a6.itp and the related Gromos FF papers.

There are 6 atom types for Nitrogen.
N peptide nitrogen (NH)
NT   terminal nitrogen (NH2)
NL   terminal nitrogen  (NH3)
NR  aromatic nitrogen
NZ  Arg NH (NH2)
NE  Arg NE (NH)

My understanding is either NT or NL but not sure which is the exact one.

Could anyone direct me about the decision of the atomic type?

Thank you
Lin
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Re: [gmx-users] Announcing: Gromacs 4.0, release candidate 1

[Nuno Azoia]

Erik Lindahl wrote:
MSVC should be able to compile it, but you'll have to create the 
makefiles/build environment yourself.


Alternatively, the easy route is to install cygwin (or get a mac ;-)

or keep your computer and run it under Linux :D
(I can not resist)

Nuno Azoia


Cheers,

Erik

On Sep 22, 2008, at 4:36 PM, Sagittarius wrote:


What compiler should I use on Windows?
Thank you in advance.

--- On *Sun, 9/21/08, Erik Lindahl /<[EMAIL PROTECTED] 
>/* wrote:


From: Erik Lindahl <[EMAIL PROTECTED] >
Subject: [gmx-users] Announcing: Gromacs 4.0, release candidate 1
To: "Discussion list for GROMACS users" mailto:gmx-users@gromacs.org>>
Date: Sunday, September 21, 2008, 11:46 PM

Stockholm, September 22 2008


In a bold move today, the Gromacs developers finally decided not to  
wait for Duke Nukem Forever before releasing Gromacs 4.0, and just put  
out release candidate 1 together with a new manual at


ftp://ftp.gromacs.org:/pub/beta/

"We realize it could be a big disappointment to many users not having  
g_dukenukemforever built-in, but sometimes you have to make hard  
decisions. Had we waited further, we might even have had to release  
Gromacs 5 before Gromacs 4", an anonymous developer said.



If you haven't already been playing around with CVS for the last year  
we think you'll be pretty impressed with the scalability of the new  
code, in addition to full checkpointing support, REMD, and various  
optimizations.


Having said that, since the code has changed a lot we decided to have  
a fairly short cycle of "release candidates" before putting out the  
real version. Please download the code above, try to compile and run  
with it (see manual and html pages in the distro for documentation of  
new stuff), and submit any bugs you find to bugzilla ("If it's not in 


bugzilla, it's not a bug").


Have fun!

Erik, Berk, and David.


  
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Erik Lindahl   <[EMAIL PROTECTED] >  Backup: 
<[EMAIL PROTECTED] >

Associate Professor, Computational Structural Biology
Center for Biomembrane Research, Dept. Biochemistry & Biophysics
Stockholm University, SE-106 91 Stockholm, Sweden
Tel: +46(0)8164675  Mobile: +46(0)703844534  Fax: mail a PDF instead








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--

Nuno Gonçalo Azoia Lopes

Laboratório de Investigação em Acabamento
Departamento de Engenharia Têxtil
Universidade do Minho
Campus de Azurém
4800-058 Guimarães
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Tel: +351 253 510 280 - Ext: 517 289
Fax: +351 253 510 293

Mobile: +351 965 382 487
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Re: [gmx-users] Search more information of Atom type: N inside the R-N(CH3)3

[Justin A. Lemkul]

Chih-Ying Lin wrote:

Hi
What is the atom type of Nitrogen inside the molecule  R-N(CH3)3  ?

I check the ffG53a5.itp and ffG53a6.itp and the related Gromos FF papers.

There are 6 atom types for Nitrogen.
N peptide nitrogen (NH)
NT   terminal nitrogen (NH2)
NL   terminal nitrogen  (NH3)
NR  aromatic nitrogen
NZ  Arg NH (NH2)
NE  Arg NE (NH)

My understanding is either NT or NL but not sure which is the exact one.

Could anyone direct me about the decision of the atomic type?


Difficult to say, because IIRC no -N(CH3)3 exists within Gromos96.  Probably the 
closest atom type is NL, based on its hybridization state and the charged nature 
of the group in question.


-Justin



Thank you
Lin
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--


Justin A. Lemkul
Graduate Research Assistant
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] Calculating Temperature from Velocity

[Andy Shelley]

I am trying to calculate the temperature from the final velocity posted in
the confout.gro file after a simulation runs. I have implemented a berendsen
thermostat to control the temperature to 300K and ran it for 1ns. Looking at
g_energy the final temperature of the system is 299.981.
Statistics over 10001 steps [ 995.0001 thru 1000.0001 ps ], 1 data sets

Energy  Average   RMSD Fluct.  Drift
Tot-Drift
---
T-System299.9811.361431.35806  0.0663083
0.331574
>From the manual section 3.4.3 the temperature can be calculated from T=
sum[mass_i v_i^2] / (#degrees of freedom * boltzmann constant) where number
of degrees of freedom=3N-N_c-N_com. I used N_com =3 because the center of
mass velocities are constants of the motion. If I only control the
temperature does this effect the number of constrants on the system? When I
calculate the temperature by hand with # degrees of freedom =3N-3 I get a
temperature of 317.5. Any ideas why I can not calculate the same temperature
g_energy does?

Thanks,
Andy
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[gmx-users] #include "ffXXX.itp"

[Chih-Ying Lin]

Hi
The command
#include "ffXXX.itp" is putting in the .top file.

I was told that this command will automatically assign the force field
parameters which I did not assign in my .top file.

I want to print out the complete force field paramters which the command
"#include "ffXXX.itp" assigned.

Would anyone direct me how to do so?

Thank you
Lin
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Re: [gmx-users] #include "ffXXX.itp"

[Justin A. Lemkul]

Chih-Ying Lin wrote:

Hi
The command
#include "ffXXX.itp" is putting in the .top file.

I was told that this command will automatically assign the force field
parameters which I did not assign in my .top file.

I want to print out the complete force field paramters which the command
"#include "ffXXX.itp" assigned.

Would anyone direct me how to do so?


You can use the -pp flag with grompp, but all that will do is print the 
parameters that are already present in the force field, and any .itp files 
you're including.  It's the same as just looking at the ff*nb/bon.itp files with 
a text editor.


Are you trying to just print this information, or cause the force field to 
assign unknown parameters?  If, for example, a certain bond type, angle type, 
etc. is not present in the force field, there is no magic way to make it appear.


-Justin



Thank you
Lin
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--


Justin A. Lemkul
Graduate Research Assistant
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] RE: Announcing: Gromacs 4.0, release candidate 1

[Vitaly Chaban]

> What compiler should I use on Windows?
> Thank you in advance.

If you succeed it would be great if you share the resulting
binaries in the internet!


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +38-097-8259698

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Re: [gmx-users] Calculating Temperature from Velocity

[Jochen Hub]

Andy Shelley wrote:
> I am trying to calculate the temperature from the final velocity posted in
> the confout.gro file after a simulation runs. I have implemented a berendsen
> thermostat to control the temperature to 300K and ran it for 1ns. Looking at
> g_energy the final temperature of the system is 299.981.
> Statistics over 10001 steps [ 995.0001 thru 1000.0001 ps ], 1 data sets
> 
> Energy  Average   RMSD Fluct.  Drift
> Tot-Drift
> ---
> T-System299.9811.361431.35806  0.0663083
> 0.331574
>>From the manual section 3.4.3 the temperature can be calculated from T=
> sum[mass_i v_i^2] / (#degrees of freedom * boltzmann constant) where number
> of degrees of freedom=3N-N_c-N_com. I used N_com =3 because the center of

You have to take bond length constraints into account (LINCS and Settle)!

Best, Jochen

> mass velocities are constants of the motion. If I only control the
> temperature does this effect the number of constrants on the system? When I
> calculate the temperature by hand with # degrees of freedom =3N-3 I get a
> temperature of 317.5. Any ideas why I can not calculate the same temperature
> g_energy does?
> 
> Thanks,
> Andy
> 
> 
> 
> 
> 
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-- 

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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[gmx-users] RE: #include "ffXXX.itp"

[Vitaly Chaban]

> I want to print out the complete force field paramters which the command
> "#include "ffXXX.itp" assigned.

Goto /usr/local/gromacs/share/gromacs/top/ on your system.

If the parameters mentioned in ffXXX.itp are redefined in your .top
you get a warning by grompp.

-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +38-097-8259698

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[gmx-users] tpbconv*

[sudheer babu]

Hi users,
I am running membrane protein simulation in between system crashed due to
power fluctuations, I am trying to extend this run by using tpbconv command
tpbconv -f 1ns.trr -e 1ns.edr -s 1ns.tpr -o new1ns.tpr
it showed that

Reading toplogy and shit from 1ns_2timeTh6_9inpopc.tpr
Reading file 1ns_2timeTh6_9inpopc.tpr, VERSION 3.3.1 (single precision)
Modifying ir->bUncStart to TRUE

READING COORDS, VELS AND BOX FROM TRAJECTORY 1ns.trr...

trn version: GMX_trn_file (single precision)
Read frame  10001: step 50 time 1000.000

Using frame of step 50 time 1000
Opened 1ns_2timeTh6_9inpopc.edr as single precision energy file
Reading frame  5 time 1000.000

READ 3 PRESSURE COUPLING MU'S FROM 1ns.edr

0 steps (0 ps) remaining from first run.
You've simulated long enough. Not writing tpr file

gcq#71: "I Want to Know Right Now" (Meatloaf)

Can anyone tell why its not writing new.tpr file
any suggestion would be appreciated
Thanks in advance.
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[gmx-users] #include "ffXXX.itp"

[Chih-Ying Lin]

HI

 The command
 #include "ffXXX.itp" is putting in the .top file.

 How does this command automatically assign the force field
 parameters which I did not assign in my .top file?

 Is it based on the atom types which I assign in my .top file?
 Then, all the force field parameters from "include ffXXX.itp"  will
give the both bonded
 and non-bonded parameters according the atom types, right?


I mean.. once I determine the atom type...such as NL and CH3..
there is a bond between NL and CH3.
But i did not assign the bond parameters in my .top file while I add
the command
"#include "ffXXX.itp" in my .top file.

Will this command #include "ffXXX.itp" automatically assign a bond
parameter for it?



Other than this, there are so many non-bonded force field parameters.
Once, I determine the atom types such as O and CR1.
But, I did not assign any non-bonded parameters for them in my .top file.
Will this command  #include "ffXXX.itp" assign all the non-bonded
force field parameters for me based on the atom types automatically?


Thank you
Lin
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[gmx-users] Re: #include "ffXXX.itp"

[Justin A. Lemkul]

Chih-Ying Lin wrote:

HI

 The command
 #include "ffXXX.itp" is putting in the .top file.

 How does this command automatically assign the force field
 parameters which I did not assign in my .top file?

 Is it based on the atom types which I assign in my .top file?
 Then, all the force field parameters from "include ffXXX.itp"  will
give the both bonded
 and non-bonded parameters according the atom types, right?


I mean.. once I determine the atom type...such as NL and CH3..
there is a bond between NL and CH3.
But i did not assign the bond parameters in my .top file while I add
the command
"#include "ffXXX.itp" in my .top file.

Will this command #include "ffXXX.itp" automatically assign a bond
parameter for it?




Yes, as long as those atoms are listed as bonded within the [ bonds ] section of 
your .top file.




Other than this, there are so many non-bonded force field parameters.
Once, I determine the atom types such as O and CR1.
But, I did not assign any non-bonded parameters for them in my .top file.
Will this command  #include "ffXXX.itp" assign all the non-bonded
force field parameters for me based on the atom types automatically?



Yes.

-Justin



Thank you
Lin



--


Justin A. Lemkul
Graduate Research Assistant
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] tpbconv*

[Justin A. Lemkul]

sudheer babu wrote:

Hi users,
I am running membrane protein simulation in between system crashed due 
to power fluctuations, I am trying to extend this run by using tpbconv 
command

tpbconv -f 1ns.trr -e 1ns.edr -s 1ns.tpr -o new1ns.tpr
it showed that

Reading toplogy and shit from 1ns_2timeTh6_9inpopc.tpr
Reading file 1ns_2timeTh6_9inpopc.tpr, VERSION 3.3.1 (single precision)
Modifying ir->bUncStart to TRUE

READING COORDS, VELS AND BOX FROM TRAJECTORY 1ns.trr...

trn version: GMX_trn_file (single precision)
Read frame  10001: step 50 time 1000.000

Using frame of step 50 time 1000
Opened 1ns_2timeTh6_9inpopc.edr as single precision energy file
Reading frame  5 time 1000.000  


READ 3 PRESSURE COUPLING MU'S FROM 1ns.edr

0 steps (0 ps) remaining from first run.
You've simulated long enough. Not writing tpr file

gcq#71: "I Want to Know Right Now" (Meatloaf)

Can anyone tell why its not writing new.tpr file
any suggestion would be appreciated
Thanks in advance.


The output message from tpbconv is pretty clear.  Frames at 1000 ps exist in 
both the .trr and .edr (also shown in the output), so it looks like your run 
actually did finish.


-Justin







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--


Justin A. Lemkul
Graduate Research Assistant
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] Forming a micelles

[Chih-Ying Lin]

Hi
I heard that it takes very long to see a micelle forming.
How long should be the simulation time to see the micelle forming?
How many nanoseconds to put on the simulation?


Is there any particular difference to simulate the micelles than other system?
My simulation steps are
1. prepare the topology files and coordinate files for the water and the solute
2. do the minimisation
3. generate the simulation box
4. put water and solute together
5. run MD with longer simulation time

Thank you
Lin
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[gmx-users] Re: Calculating Temperature from Velocity

[Andy Shelley]

A few more questions added to my first response.  When calculating the
Temperature should I use the mass of the molecule or of the atoms times the
velocity of the atoms or velocity of the molecule? Also, when looking at the
output of g_traj if I create a small group of atoms close to each other, say
10-12 atoms, the temperature of these atoms varies alot while the
temperature the whole system does not, why is this?  Is there a way to
accurately determine the temperature of a small number of atoms?

Thanks again,
Andy

On Mon, Sep 22, 2008 at 10:42 AM, Andy Shelley <[EMAIL PROTECTED]>wrote:

> I am trying to calculate the temperature from the final velocity posted in
> the confout.gro file after a simulation runs. I have implemented a berendsen
> thermostat to control the temperature to 300K and ran it for 1ns. Looking at
> g_energy the final temperature of the system is 299.981.
> Statistics over 10001 steps [ 995.0001 thru 1000.0001 ps ], 1 data sets
>
> Energy  Average   RMSD Fluct.  Drift
> Tot-Drift
>
> ---
> T-System299.9811.361431.35806  0.0663083
> 0.331574
> From the manual section 3.4.3 the temperature can be calculated from T=
> sum[mass_i v_i^2] / (#degrees of freedom * boltzmann constant) where number
> of degrees of freedom=3N-N_c-N_com. I used N_com =3 because the center of
> mass velocities are constants of the motion. If I only control the
> temperature does this effect the number of constrants on the system? When I
> calculate the temperature by hand with # degrees of freedom =3N-3 I get a
> temperature of 317.5. Any ideas why I can not calculate the same temperature
> g_energy does?
>
> Thanks,
> Andy
>
>
>
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[gmx-users] RE: #include "ffXXX.itp"

[Vitaly Chaban]

>  How does this command automatically assign the force field
>  parameters which I did not assign in my .top file?

It inserts the content of ffXXX.itp into .top file.


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +38-097-8259698

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[gmx-users] Re: #include "ffXXX.itp"

[Chih-Ying Lin]

Hi
>From Justin:
 " Yes, as long as those atoms are listed as bonded within the [ bonds ]
 section of your .top file. "

The specific "bonded function", such as gb_28",  should be also listed
on the [bonds] section, right?

Or, it could assign NOTHING for me, right?

so,
[bonds]
; ai  aj  funct
8 9 gb_28
is correct...


[bonds]
; ai  aj  funct
8 9
is INCORECT...  and 8 , 9 will NOT be automatically bonded,  right?

The same for the nonbonded parts, right?
Thank you
Lin








On 9/22/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
>
>  Chih-Ying Lin wrote:
>
> > HI
> >
> >  The command
> >  #include "ffXXX.itp" is putting in the .top file.
> >
> >  How does this command automatically assign the force field
> >  parameters which I did not assign in my .top file?
> >
> >  Is it based on the atom types which I assign in my .top file?
> >  Then, all the force field parameters from "include ffXXX.itp"  will
> > give the both bonded
> >  and non-bonded parameters according the atom types, right?
> >
> >
> > I mean.. once I determine the atom type...such as NL and CH3..
> > there is a bond between NL and CH3.
> > But i did not assign the bond parameters in my .top file while I add
> > the command
> > "#include "ffXXX.itp" in my .top file.
> >
> > Will this command #include "ffXXX.itp" automatically assign a bond
> > parameter for it?
> >
> >
> >
>
>  Yes, as long as those atoms are listed as bonded within the [ bonds ]
> section of your .top file.
>
>
> >
> > Other than this, there are so many non-bonded force field parameters.
> > Once, I determine the atom types such as O and CR1.
> > But, I did not assign any non-bonded parameters for them in my .top file.
> > Will this command  #include "ffXXX.itp" assign all the non-bonded
> > force field parameters for me based on the atom types automatically?
> >
> >
>
>  Yes.
>
>  -Justin
>
>
> >
> > Thank you
> > Lin
> >
> >
>
>  --
>  
>
>  Justin A. Lemkul
>  Graduate Research Assistant
>  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] Re: Calculating Temperature from Velocity

[Vitaly Chaban]

Hi Andy,

> I create a small group of atoms close to each other, say
> 10-12 atoms, the temperature of these atoms varies alot while the
> temperature the whole system does not, why is this?

A mob is always uniform. :) You have a normal situation indeed.

>  Is there a way to
> accurately determine the temperature of a small number of atoms?

To make many-many simulations and then average.


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +38-097-8259698

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[gmx-users] RE: Forming a micelles

[Vitaly Chaban]

> I heard that it takes very long to see a micelle forming.

I believe it's quite true.

> How long should be the simulation time to see the micelle forming?
> How many nanoseconds to put on the simulation?

I suggest you to use ngmx (or VMD) to monitor the trajectory and catch
the moment you are interested in.


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +38-097-8259698

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[gmx-users] The box size and the # of the solute / water molecules?

[Chih-Ying Lin]

Hi
What size of the simulation system can be really represent the real situation?

Once I decide the box size,
the water density can determine the # of water molecules to put in.
And, the concentration can determine the # of the solute to put in.

Is the procedure correct?

Thank you
Lin
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[gmx-users] Re: #include "ffXXX.itp"

[Justin A. Lemkul]

Chih-Ying Lin wrote:


so,
[bonds]
; ai  aj  funct
8 9 gb_28
is correct...




No.  The function type is not the same as a bond type.  Read in Chapter 5 about 
the difference.  If you have atoms 8 and 9 as a bond, with the appropriate 
function type, the grompp will assign the values associated with gb_28 to that bond.




[bonds]
; ai  aj  funct
8 9
is INCORECT...  and 8 , 9 will NOT be automatically bonded,  right?



Right, that is *also* incorrect.

Perhaps it would be beneficial for you to run through some tutorials with simple 
proteins to see topologies that are automatically generated and how they work.


-Justin


The same for the nonbonded parts, right?
Thank you
Lin








On 9/22/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:


 Chih-Ying Lin wrote:


HI

 The command
 #include "ffXXX.itp" is putting in the .top file.

 How does this command automatically assign the force field
 parameters which I did not assign in my .top file?

 Is it based on the atom types which I assign in my .top file?
 Then, all the force field parameters from "include ffXXX.itp"  will
give the both bonded
 and non-bonded parameters according the atom types, right?


I mean.. once I determine the atom type...such as NL and CH3..
there is a bond between NL and CH3.
But i did not assign the bond parameters in my .top file while I add
the command
"#include "ffXXX.itp" in my .top file.

Will this command #include "ffXXX.itp" automatically assign a bond
parameter for it?




 Yes, as long as those atoms are listed as bonded within the [ bonds ]
section of your .top file.



Other than this, there are so many non-bonded force field parameters.
Once, I determine the atom types such as O and CR1.
But, I did not assign any non-bonded parameters for them in my .top file.
Will this command  #include "ffXXX.itp" assign all the non-bonded
force field parameters for me based on the atom types automatically?



 Yes.

 -Justin



Thank you
Lin



 --
 

 Justin A. Lemkul
 Graduate Research Assistant
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 





--


Justin A. Lemkul
Graduate Research Assistant
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] Two independent umbrellas in gromacs 3.3.1

[chris . neale]

Here are some source code modifications that allow two reference  
groups for the pull code (umbrella option). It would be simple to mod  
this for more than two groups. It would be slightly more difficult to  
enable all pull options (e.g. constraints) with more than one  
reference group, as that may require modification to update() (and one  
other function whose name escapes me) in some cases.


For usage, on would have, in addition to x.ppa, a file called x.ppa2.  
I have only tested it when there is one pulled group per reference  
group.


I used gromacs 3.3.1 as my base code. Based on the .pdf manual  
recently made available for gromacs 4, this option does not appear to  
be currently available for gromacs 4, and I didn't invest any time to  
see how difficult it would be to add this.


Hope it is useful,
Chris.

###

$diff orig/src/kernel/md.c new/src/kernel/md.c
329c329
<   t_pull pulldata; /* for pull code */
---

  t_pull pulldata,pulldata_refTwo; /* for pull code */

397a398,400
   
init_pull(log,nfile,fnm,&pulldata_refTwo,state->x,mdatoms,inputrec->opts.nFreeze,

state->box,START(nsb),HOMENR(nsb),cr);


693c696
<   (pulldata.runtype == eAfm || pulldata.runtype == eUmbrella))
---

  (pulldata.runtype == eAfm || pulldata.runtype == eUmbrella)){

696a700,703

  pull(&pulldata_refTwo,state->x,f,force_vir,state->box,
   top,inputrec->delta_t,step,t,
   mdatoms,START(nsb),HOMENR(nsb),cr);
}


###

$diff orig/src/mdlib/pullinit.c new/src/mdlib/pullinit.c
223a224

  static int timesCalled=0;

230a232,235
  char tempfnmpi[256],tempfnmpo[256],tempfnmpd[256]; /*part of the  
double pull reference hack */



  timesCalled++;

241c246,256
<   read_pullparams(pull, opt2fn("-pi",nfile,fnm), opt2fn("-po",nfile,fnm));
---

  if(timesCalled==1){
sprintf(tempfnmpi,"%s",opt2fn("-pi",nfile,fnm));
sprintf(tempfnmpo,"%s",opt2fn("-po",nfile,fnm));
sprintf(tempfnmpd,"%s",opt2fn("-pd",nfile,fnm));
  }else{
sprintf(tempfnmpi,"%s2",opt2fn("-pi",nfile,fnm));
sprintf(tempfnmpo,"%s2",opt2fn("-po",nfile,fnm));
sprintf(tempfnmpd,"%s2",opt2fn("-pd",nfile,fnm));
  }

  read_pullparams(pull, tempfnmpi, tempfnmpo);

248c263
< char * filename = opt2fn("-pd", nfile, fnm);
---

char * filename = tempfnmpd;

250c265
< pull->out = ffopen(opt2fn("-pd",nfile,fnm),"w");
---

pull->out = ffopen(tempfnmpd,"w");


###

Code changes finished.

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Re: [gmx-users] Forming a micelles

[David van der Spoel]

Chih-Ying Lin wrote:

Hi
I heard that it takes very long to see a micelle forming.
How long should be the simulation time to see the micelle forming?
How many nanoseconds to put on the simulation?


Is there any particular difference to simulate the micelles than other system?
My simulation steps are
1. prepare the topology files and coordinate files for the water and the solute
2. do the minimisation
3. generate the simulation box
4. put water and solute together
5. run MD with longer simulation time


@Article{ Marrink2000a,
  author =   "S. J. Marrink and D. P. Tieleman and A. E. Mark",
  title ="Molecular dynamics simulation of the kinetics of
  spontaneous micelle formation",
  journal =  "J Phys Chem B",
  year = 2000,
  volume =   104,
  pages ="12165-12173"
}





Thank you
Lin
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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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Re: [gmx-users] tpbconv*

[Jochen Hub]

sudheer babu wrote:
> Hi users,
> I am running membrane protein simulation in between system crashed due to
> power fluctuations, I am trying to extend this run by using tpbconv command
> tpbconv -f 1ns.trr -e 1ns.edr -s 1ns.tpr -o new1ns.tpr
> it showed that
> 
> Reading toplogy and shit from 1ns_2timeTh6_9inpopc.tpr
> Reading file 1ns_2timeTh6_9inpopc.tpr, VERSION 3.3.1 (single precision)
> Modifying ir->bUncStart to TRUE
> 
> READING COORDS, VELS AND BOX FROM TRAJECTORY 1ns.trr...
> 
> trn version: GMX_trn_file (single precision)
> Read frame  10001: step 50 time 1000.000
> 
> Using frame of step 50 time 1000
> Opened 1ns_2timeTh6_9inpopc.edr as single precision energy file
> Reading frame  5 time 1000.000
> 
> READ 3 PRESSURE COUPLING MU'S FROM 1ns.edr
> 
> 0 steps (0 ps) remaining from first run.
> You've simulated long enough. Not writing tpr file

  ^^^
Use -until or -extend (in latest gromacs) if you want to simulate longer.

best, Jochen



> 
> gcq#71: "I Want to Know Right Now" (Meatloaf)
> 
> Can anyone tell why its not writing new.tpr file
> any suggestion would be appreciated
> Thanks in advance.
> 
> 
> 
> 
> 
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-- 

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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