Re: [gmx-users] Trjconv trouble

[Mark Abraham]

Tsjerk Wassenaar wrote:

Hi Guy,

Which version are you using? It may be there's a flaw in the code. If
you want the forces in human readable format, you can also try
converting the .trr to .g96


Moreover you can see if they exist in the .trr file by using gmxdump.

Mark


On Mon, Sep 28, 2009 at 9:59 PM, Vigers, Guy
 wrote:

Dear Gromacs users,



I seem to be having trouble with trjconv.  I have run a short simulation
and want to write out a trajectory with positions and forces.  However, when
using trjconv to write out the trajectory I get the same result whether I
try and write out velocities or forces:




mpirun -np 2 mdrun -np 2 -v -deffnm pr1
trjconv -f pr1.trr -s pr1.tpr -force -b 30 -e 40 -o test1.gro
trjconv -f pr1.trr -s pr1.tpr -vel -b 30 -e 40 -o test2.gro




head -5 test1.gro

Generated by trjconv : Protein in water t=  30.0

61767

  331SOL OW1   0.745   1.223   1.235 -0.8542  0.4057 -0.0772

  331SOLHW12   0.662   1.257   1.197 -0.0011  2.1431 -1.5672

  331SOLHW23   0.803   1.297   1.208  1.5836 -1.7723 -2.4831




head -5 test2.gro

Generated by trjconv : Protein in water t=  30.0

61767

  331SOL OW1   0.745   1.223   1.235 -0.8542  0.4057 -0.0772

  331SOLHW12   0.662   1.257   1.197 -0.0011  2.1431 -1.5672

  331SOLHW23   0.803   1.297   1.208  1.5836 -1.7723 -2.4831





Here are the relevant lines from my .mdp file:



; ** Options for Output Control **

nstxout = 100

nstvout = 100

nstfout = 100

;Output freq for energies to log and energy files

nstlog  = 100

nstenergy   = 100

;



I get equivalent results whether I do all or part of the trajectory and
whether I write out the whole system or just one part.  As you can see from
the .mdp file, I am using the same output frequencies for everything.  I am
running Gromacs 4.0.5



Can anyone tell me what I'm doing wrong?  I apologize if it is a boneheaded
error.



Thank you in advance



Guy Vigers





(please ignore the boilerplate below:)



This electronic message transmission is a PRIVATE communication which
contains information which may be confidential or privileged. The
information is intended to be for the use of the individual or entity
named above. If you are not the intended recipient, please be aware that
any disclosure, copying, distribution or use of the contents of this
information is prohibited. Please notify the sender of the delivery
error by replying to this message, or notify us by telephone
(877-633-2436, ext. 0), and then delete it from your system.

___
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!
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

Re: [gmx-users] Trjconv trouble

[Tsjerk Wassenaar]

Hi Guy,

Which version are you using? It may be there's a flaw in the code. If
you want the forces in human readable format, you can also try
converting the .trr to .g96

Hope it helps,

Tsjerk

On Mon, Sep 28, 2009 at 9:59 PM, Vigers, Guy
 wrote:
> Dear Gromacs users,
>
>
>
>     I seem to be having trouble with trjconv.  I have run a short simulation
> and want to write out a trajectory with positions and forces.  However, when
> using trjconv to write out the trajectory I get the same result whether I
> try and write out velocities or forces:
>
>
>
>> mpirun -np 2 mdrun -np 2 -v -deffnm pr1
>
>> trjconv -f pr1.trr -s pr1.tpr -force -b 30 -e 40 -o test1.gro
>
>> trjconv -f pr1.trr -s pr1.tpr -vel -b 30 -e 40 -o test2.gro
>
>
>
>> head -5 test1.gro
>
> Generated by trjconv : Protein in water t=  30.0
>
> 61767
>
>   331SOL OW    1   0.745   1.223   1.235 -0.8542  0.4057 -0.0772
>
>   331SOL    HW1    2   0.662   1.257   1.197 -0.0011  2.1431 -1.5672
>
>   331SOL    HW2    3   0.803   1.297   1.208  1.5836 -1.7723 -2.4831
>
>
>
>> head -5 test2.gro
>
> Generated by trjconv : Protein in water t=  30.0
>
> 61767
>
>   331SOL OW    1   0.745   1.223   1.235 -0.8542  0.4057 -0.0772
>
>   331SOL    HW1    2   0.662   1.257   1.197 -0.0011  2.1431 -1.5672
>
>   331SOL    HW2    3   0.803   1.297   1.208  1.5836 -1.7723 -2.4831
>
>
>
>
>
> Here are the relevant lines from my .mdp file:
>
>
>
> ; ** Options for Output Control **
>
> nstxout = 100
>
> nstvout = 100
>
> nstfout = 100
>
> ;    Output freq for energies to log and energy files
>
> nstlog  = 100
>
> nstenergy   = 100
>
> ;
>
>
>
> I get equivalent results whether I do all or part of the trajectory and
> whether I write out the whole system or just one part.  As you can see from
> the .mdp file, I am using the same output frequencies for everything.  I am
> running Gromacs 4.0.5
>
>
>
> Can anyone tell me what I'm doing wrong?  I apologize if it is a boneheaded
> error.
>
>
>
> Thank you in advance
>
>
>
> Guy Vigers
>
>
>
>
>
> (please ignore the boilerplate below:)
>
>
>
> This electronic message transmission is a PRIVATE communication which
> contains information which may be confidential or privileged. The
> information is intended to be for the use of the individual or entity
> named above. If you are not the intended recipient, please be aware that
> any disclosure, copying, distribution or use of the contents of this
> information is prohibited. Please notify the sender of the delivery
> error by replying to this message, or notify us by telephone
> (877-633-2436, ext. 0), and then delete it from your system.
>
> ___
> gmx-users mailing list    gmx-us...@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
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
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

Re: [gmx-users] Error message: Cut-off length is longer than half the shortest box vector

[Mark Abraham]

Lum Nforbi wrote:

Hello everyone,
  Thanks to Tsjerk, Mark Abraham, Justin and Dr. Vitaly for the very 
useful inputs to my quest for generating a .gro file from a .pdb file.
  I am now trying to minimize the energy of the system so I can do 
an mdrun but I keep having the error message:
the cut-off length is longer than half the shortest box vector or longer 
than the smallest box diagonal element. Increase the box size or 
decrease rlist.
  I have changed the values of rlist, rvdw and rcoulomb, 


Don't, unless you know what you're doing. Your force field is 
parametrized under certain conditions, and varying these quantities by 
much will remove you from conditions where the force field might be 
supposed to work well. It does sound like you would benefit from doing 
some general background reading about molecular mechanics force fields 
and molecular dynamics simulations, and/or some more tutorial material.


and even 
the box size several times but I still keep having this message. Please, 


You can change your box size with editconf, and then you will need to 
use genconf (or other) to increase the amount of solvent.



I need help to figure out what to do to fix this problem.
The command line I am using is:grompp -f waters.mdp -c waters_b.gro -p 
water.top -o watersinput.tpr


This command generates a (binary) run input file. It does not do 
anything to the box size, which it reads from the -c file.


  Also, is there a way to convert atom types from one format to 
another? I also have the following warnings:


"Warning: atom name 1 in water.top and waters_b.gro does not match (OW - O)
Warning: atom name 2 in water.top and waters_b.gro does not match (HW1 - H)
Warning: atom name 3 in water.top and waters_b.gro does not match (HW2 - H)
atom names from water.top will be used
atom names from waters_b.gro will be ignored."

I had drawn my molecule in ghemical and exported as a pdb file and so 
the atom types O and H were automatically generated.


Using the coordinate file output from pdb2gmx for subsequent operations 
is the correct way to avoid these warnings. If you're not using pdb2gmx 
then you need to really understand what you're doing.


Mark
___
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

Re: [gmx-users] Error message: Cut-off length is longer than half the shortest box vector

[Justin A. Lemkul]

Lum Nforbi wrote:

Hello everyone,
  Thanks to Tsjerk, Mark Abraham, Justin and Dr. Vitaly for the very 
useful inputs to my quest for generating a .gro file from a .pdb file.
  I am now trying to minimize the energy of the system so I can do 
an mdrun but I keep having the error message:
the cut-off length is longer than half the shortest box vector or longer 
than the smallest box diagonal element. Increase the box size or 
decrease rlist.
  I have changed the values of rlist, rvdw and rcoulomb, and even 
the box size several times but I still keep having this message. Please, 
I need help to figure out what to do to fix this problem.


This should be a very simple problem to fix.  You shouldn't haphazardly change 
the cutoff values.  Doing so can have a very negative impact on your results. 
If the smallest box vector (at the bottom of the .gro file) is less than 2 * 
longest cutoff, then you are not satisfying the minimum image convention for a 
periodic system.  Increase the size of your system.


The command line I am using is:grompp -f waters.mdp -c waters_b.gro -p 
water.top -o watersinput.tpr


  Also, is there a way to convert atom types from one format to 
another? I also have the following warnings:


"Warning: atom name 1 in water.top and waters_b.gro does not match (OW - O)
Warning: atom name 2 in water.top and waters_b.gro does not match (HW1 - H)
Warning: atom name 3 in water.top and waters_b.gro does not match (HW2 - H)
atom names from water.top will be used
atom names from waters_b.gro will be ignored."

I had drawn my molecule in ghemical and exported as a pdb file and so 
the atom types O and H were automatically generated.




Probably not a big deal in this case, since you just have water, but in general, 
you structure file should match the topology with respect to atom names.  More 
complex systems can have very negative consequences when this happens.


-Justin



Thank you,
Lum






___
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


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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_lists/users.php

[gmx-users] Error message: Cut-off length is longer than half the shortest box vector

[Lum Nforbi]

Hello everyone,
  Thanks to Tsjerk, Mark Abraham, Justin and Dr. Vitaly for the very
useful inputs to my quest for generating a .gro file from a .pdb file.
  I am now trying to minimize the energy of the system so I can do an
mdrun but I keep having the error message:
the cut-off length is longer than half the shortest box vector or longer
than the smallest box diagonal element. Increase the box size or decrease
rlist.
  I have changed the values of rlist, rvdw and rcoulomb, and even the
box size several times but I still keep having this message. Please, I need
help to figure out what to do to fix this problem.
The command line I am using is:grompp -f waters.mdp -c waters_b.gro -p
water.top -o watersinput.tpr

  Also, is there a way to convert atom types from one format to another?
I also have the following warnings:

"Warning: atom name 1 in water.top and waters_b.gro does not match (OW - O)
Warning: atom name 2 in water.top and waters_b.gro does not match (HW1 - H)
Warning: atom name 3 in water.top and waters_b.gro does not match (HW2 - H)
atom names from water.top will be used
atom names from waters_b.gro will be ignored."

I had drawn my molecule in ghemical and exported as a pdb file and so the
atom types O and H were automatically generated.


Thank you,
Lum
___
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

Re: [gmx-users] error in converting charmm to gromacs

[Mark Abraham]

Chanchal wrote:
> Hi Mark,
>   Sorry for off-the-list email. Actually I sent an email to the list 
but due the large size it is not sent.
>  Currently I am working on DOPC membrane simulation. I have built the 
membrane in www.charmm-gui.org  website. I 
am using your scripts  to convert par_all27_prot_lipid.prm to 
charmmbon.itp and charmmnb.itp. When I tried the script 
convert_charmm_to_gromacs.pl (version 1.2) on par_all27_prot_lipid.prm I 
got the message "Sin of delta not zero, hope this is the only dihedral of

>  type XCSSS X
>  (sin delta = 0.00349065141522373).

The documentation inside my scripts deal with this. The warning message 
is normal.


> I found that ffcharmmnb.itp has only 40 line starting with Cs and 
ends with HT. There are no entries for any atom types other than carbon
> and hydrogen. Is it correct? Please find attached *.itp. Please 
someone shed light on it.


It may be correct - I can't be sure of the contents of the input file. 
If it only had these lipid atom types, then the results are correct. If 
it had other types, then the behaviour looks to be erroneous. Also, what 
version of my script were you using?


>  I placed these *.itp files into the direcotry: 
/home/users/parimalk/software/
> gromacs-4.0.5/share/gromacs/top. Then I executed the command: 
pdb2gmx_d -ff charmm -f step5_assembly.pdb -p topol.top to create the 
topology .

>
> I got the error message : Program pdb2gmx_d, VERSION 4.0.5
> Source code file: futil.c, line: 527
>
> Fatal error:
> Library file ffcharmm.rtp not found in current dir nor in default 
directories.

> (You can set the directories to search with the GMXLIB path variable)
>
> How can I get the ffcharmm.rtp file?? I was looking  gromacs archives 
and the link given there is not working now. Can someone help me to fix 
this error and provide the *.rtp file?


Per my documentation, I don't provide an .rtp file, since I've never 
written one. Yuguang Mu's CHARMM port did provide one, and the 
not-really-supported CHARMM port in GROMACS 4.0.5 also provides one. In 
all cases, as I posted on gmx-users just yesterday, one needs to edit 
${GMXLIB}/FF.dat to have a line for CHARMM and update the total number 
of force fields available.


Mark

___
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] error in converting charmm to gromacs

[Chanchal]

Hi All,
I already had sent this email to the list. But since I attached some
files to it, it is not sent to the list. It is under moderator approval. So
I am sending this email without any attachment.
   Currently I am working on DOPC membrane simulation. I have built the
membrane in www.charmm-gui.org website. I am using Mark Abraham's charmm to
gromacs script to convert par_all27_prot_lipid.prm to charmmbon.itp and
charmmnb.itp. When I tried the script convert_charmm_to_gromacs.pl (version
1.2) on par_all27_prot_lipid.prm I got the message "Sin of delta not zero,
hope this is the only dihedral of
 type XCSSS X
 (sin delta = 0.00349065141522373).

I found that ffcharmmnb.itp has only 40 line starting with Cs and ends with
HT. There are no entries for any atom types other than carbon
and hydrogen. Is it correct?  Please someone shed light on it.
 I placed these *.itp files into the direcotry:
/home/users/parimalk/software/gromacs-4.0.5/share/gromacs/top. Then I
executed the command:  pdb2gmx_d -ff charmm -f step5_assembly.pdb -p
topol.top to create the topology .

I got the error message : Program pdb2gmx_d, VERSION 4.0.5
Source code file: futil.c, line: 527

Fatal error:
Library file ffcharmm.rtp not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path variable)

How can I get the ffcharmm.rtp file?? I was looking  gromacs archives and
the link given there is not working now. Can someone help me to fix this
error and provide the *.rtp file?
Thanks
Chanchal
___
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

Re: [gmx-users] Re: Re: Re: Re: Re: Re: umbrella potential

[Justin A. Lemkul]

Stefan Hoorman wrote:



I have included in my simulation some windows past the ~2nm distance 
between the two groups. The same result occurred, but with a longer 
separation, the graphic seems to continue rising and the histogram looks 
even taller. Here are the links for the profile.xvg, histogram.xvg and 
the rapidshare link for my histogram.xvg file in case you want to have a 
look.
histogram link > 
"http://i784.photobucket.com/albums/yy123/stefhoor/histogram_longer.jpg";
profile link > 
"http://i784.photobucket.com/albums/yy123/stefhoor/profile_longer.jpg";

histogram text file > "http://rapidshare.com/files/286236452/histo.xvg.html";
The histogram file looks like a diagonal matrix of 200X20, in which the 
"diagonal" range is of approximately 10 lines, i.e., the first collumn 
has 10 lines of non-zero entries and then 190 of zeros, the second 
collumn has 12 lines of non-zeros, the third has the first three lines 
of zero entries and then 10 or 12 lines of non-zeros and then lots of 
zeros again, and so on and so forth.


Right, there are multiple datasets in the histo.xvg file.  However you're 
plotting it (i.e., the image linked above) is not correct.  See here for a 
proper look at your histograms:


http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Images/Gromacs/histo_sh.jpg

I suppose the histograms look good; I don't see anything horrendously wrong that 
would give weird behavior.


Do you have sufficient space in your box to do this pulling?  Could you be 
running into periodicity effects?  Have you tried doing a 1-D pull instead of 
pulling in two dimensions, as I suggested before?


-Justin

In case you prefer another way for me to show you the histogram text 
file, please let me know.

Thank you




___
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


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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_lists/users.php

[gmx-users] Re: Re: Re: Re: Re: Re: umbrella potential

[Stefan Hoorman]

>
>
> > To generate each window I use "trjconv -f
> > original_separation_trajectory.xtc -s topol.tpr -dump
> > time_where_specific_distance_is_found -o
> > frame_where_separation_between_structures_is_x.gro"
> > Once I have the coordinate files regarding this specific distance
> > between my pull groups, I simulate each of them (using the same
> > topol.top file, index.ndx...etc) but with the new md_pull.mdp file I've
> > shown here earlier.
> > Is this wrong for wham analysis?
>
> This should be right, hence my confusion about the histogram.  Are you sure
> there's only one peak?  Have you looked at it with a text editor?  There
> should
> be multiple entries in the file, one for each window that you're
> simulating?
>
> -Justin
>
> > Thank you
>

I have included in my simulation some windows past the ~2nm distance between
the two groups. The same result occurred, but with a longer separation, the
graphic seems to continue rising and the histogram looks even taller. Here
are the links for the profile.xvg, histogram.xvg and the rapidshare link for
my histogram.xvg file in case you want to have a look.
histogram link > "
http://i784.photobucket.com/albums/yy123/stefhoor/histogram_longer.jpg";
profile link > "
http://i784.photobucket.com/albums/yy123/stefhoor/profile_longer.jpg";
histogram text file > "http://rapidshare.com/files/286236452/histo.xvg.html";
The histogram file looks like a diagonal matrix of 200X20, in which the
"diagonal" range is of approximately 10 lines, i.e., the first collumn has
10 lines of non-zero entries and then 190 of zeros, the second collumn has
12 lines of non-zeros, the third has the first three lines of zero entries
and then 10 or 12 lines of non-zeros and then lots of zeros again, and so on
and so forth.
In case you prefer another way for me to show you the histogram text file,
please let me know.
Thank you
___
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] Trjconv trouble

[Vigers, Guy]

Dear Gromacs users,

 

I seem to be having trouble with trjconv.  I have run a short
simulation and want to write out a trajectory with positions and forces.
However, when using trjconv to write out the trajectory I get the same
result whether I try and write out velocities or forces:

 

> mpirun -np 2 mdrun -np 2 -v -deffnm pr1

> trjconv -f pr1.trr -s pr1.tpr -force -b 30 -e 40 -o test1.gro

> trjconv -f pr1.trr -s pr1.tpr -vel -b 30 -e 40 -o test2.gro

 

> head -5 test1.gro

Generated by trjconv : Protein in water t=  30.0

61767

  331SOL OW1   0.745   1.223   1.235 -0.8542  0.4057 -0.0772

  331SOLHW12   0.662   1.257   1.197 -0.0011  2.1431 -1.5672

  331SOLHW23   0.803   1.297   1.208  1.5836 -1.7723 -2.4831

  

> head -5 test2.gro

Generated by trjconv : Protein in water t=  30.0

61767

  331SOL OW1   0.745   1.223   1.235 -0.8542  0.4057 -0.0772

  331SOLHW12   0.662   1.257   1.197 -0.0011  2.1431 -1.5672

  331SOLHW23   0.803   1.297   1.208  1.5836 -1.7723 -2.4831

 

 

Here are the relevant lines from my .mdp file:

 

; ** Options for Output Control **

nstxout = 100 

nstvout = 100 

nstfout = 100

;Output freq for energies to log and energy files

nstlog  = 100

nstenergy   = 100

;

 

I get equivalent results whether I do all or part of the trajectory and
whether I write out the whole system or just one part.  As you can see
from the .mdp file, I am using the same output frequencies for
everything.  I am running Gromacs 4.0.5

 

Can anyone tell me what I'm doing wrong?  I apologize if it is a
boneheaded error.

 

Thank you in advance

 

Guy Vigers

 

 

(please ignore the boilerplate below:)

 



This electronic message transmission is a PRIVATE communication which
contains information which may be confidential or privileged. The
information is intended to be for the use of the individual or entity
named above. If you are not the intended recipient, please be aware that
any disclosure, copying, distribution or use of the contents of this
information is prohibited. Please notify the sender  of the delivery
error by replying to this message, or notify us by telephone
(877-633-2436, ext. 0), and then delete it from your system.___
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

Re: [gmx-users] Generating a .gro file from .pdb file

[Tsjerk Wassenaar]

Hi,

> No, that procedure generates a topology file, it is not the correct tool for
> a change of coordinate format (which is almost never needed anyway). As a
> side effect, it regularizes an input coordinate file which might have been
> in one of various formats, and outputs a coordinate file whose default
> format happens to be .gro (but could be a range of possibilities). I wish
> tutorial writers would not give new people the wrong impression about the
> purpose of this step!
>

>From my tutorial (http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html):

Structure conversion and topology

A molecule is defined by the coordinates of the atoms as well as by a
description of the bonded and nonbonded interactions. Since the
structure obtained from the PDB only contains coordinates, we first
have to construct the topology, which describes the system in terms of
atom types, charges, bonds, etc. This topology is specific to a
certain force field and the force field to be used is one of the
issues requiring careful consideration. Here we use the GROMOS96 53a6
united atom force field, which is parameterized to give good
predictions of free energies of solvation of amino acid side chains
and which generally gives good agreement with NMR experiments.
It is important that the topology matches with the structure, which
means that the structure needs to be converted too, to adhere to the
force field used. To convert the structure and construct the topology,
the program pdb2gmx can be used. This program is designed to build
topologies for molecules consisting of distinct building blocks, such
as amino acids. It uses a library of building blocks for the
conversion and will fail to recognize molecules or residues not
present in the library. Issue the following command to convert the
structure; choose the GROMOS 53a6 force field when prompted. Note the
flag -ignh, which causes hydrogen atoms present in the file to be
removed, and to be rebuild according to the description in the force
field.

pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh

Read through the output on the screen and check the choices made for
the histidine protonation and the resulting total charge of the
protein. Also browse through the input structure file (protein.pdb,
pdb format) and output structure file (protein.gro, gromacs format).
Note the differences between the two formats. Also note that the
output structure file could as well have been chosen to be in pdb
format. Now browse through the topology file and look at the
structure.

Write down the number of atoms before and after the conversion and
explain the difference

List the atoms, atom types and charges from a tyrosine residue as
given in the topology file

###

TAW

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
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] integration protein-bilayer in CG

[Francesco Pietra]

Hi:

I am looking for indications how to insert a large trimer CG protein
into one of the pre-equilibrated bilayers (preferably POPC, if it
exists) of the MARTINI web site. And surround the whole with a layer
of water, if possible. I have already prepared the .itp file for the
trimer, that is, if I did correctly, the CG knows the secondary
structure of the trimer..

New to both GROMACS and MARTINI, I have experience how to that job
all-atoms with AMBER. There, a cavity into the hydrated bilayer is
first created, shaped on the protein to host.

For the moment I am at GROMACS 3.3 on a parallel machine.

Thanks for help

francesco pietra
___
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] gyrate -p

[nicegromacs]

Hi gmx-users,

With respect to g_gyrate, Which is the algorithm difference between the default 
output and output with -p in g_gyrate? I have plotted both outputs one with -f 
-s -o and other with -f -s -o -p and the graphics are very different between 
both outputs

Thank you in advance

veduardo.

Lab. de  Fisicoquímica Molecular

Facultas de Ciencias

Universidad de Chile

 


___
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

Re: [gmx-users] nvt.gro

[ram bio]

Dear Justin,

Thanks for the options and suggestions, will be back after some trials with
modelled proteins.

Ram

On Mon, Sep 28, 2009 at 6:17 PM, Justin A. Lemkul  wrote:

>
>
> ram bio wrote:
>
>> Dear Justin,
>>
>> When I used the energy mininized system for NPT annealing with position
>> restraints on lipids and there was no separation. So, I think I can proceed
>> now to equiliration phase 2 (1-ns NPT equilibration-NPT) and then run the
>> Molecular Dynamics for data collection(1ns).What do you suggest, is it the
>> right way i am following..as i will be not be using NVT equillibration
>> anywhere through out the process.
>>
>>
> I think that should be fine.  There is really no prescribed way to do
> equilibration, necessarily.  Everyone has their own method.  If you can
> stabilize the temperature and pressure prior to data collection, then you've
> done enough, in general.  Just be aware that my definition of "data
> collection" simply means that you're remove restraints from anything that
> was previously restrained.  Collecting data for membrane protein systems
> often occurs after 10-20 ns (or more), to allow for re-orientation of
> lipids, which is very slow.
>
> -Justin
>
>  Thanks,
>>
>> Ram
>>
>>
>> On Fri, Sep 25, 2009 at 11:23 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>ram bio wrote:
>>
>>Dear Justin,
>>
>>As suggested, i increased the force constant in the Z dimension
>>from 1000 to 1, and did the NVT equillibration, but still
>>the gap existed, then i gave the output of nvt equillibration
>>that is nvt.gro as input for the NPT anneling simulation
>>(suggested as with position constraints, 1000) and simulated and
>>here also i had gap .between layers when npt.gro was viewed in VMD.
>>
>>I have a query that is can I use nvt equllibrated system as
>>input for NPT simualated annealing or should I use the initial
>>ionized and minimized system for the NPT annaelated simulation,
>>as the gap is still persisting...
>>
>>
>>Use the energy-minimized system as the input into annealing.  I have
>>no idea why this separation would be happening in this system,
>>unless the box has been prepared improperly.  I chose the KALP-DPPC
>>system because it is very robust in everything we've tried to
>>subject it to.
>>
>>-Justin
>>
>>Thanks
>>
>>Ram
>>
>>
>>On Thu, Sep 24, 2009 at 4:16 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   ram bio wrote:
>>
>>   Dear Justin,
>>
>>   As suggested in the tutorial by you i applied the lipid
>>position
>>   restraints, while running the NVT  equillibration, but
>>after the
>>   job is finished, when i observed the nvt.gro file in VMD,
>>still
>>   there is a gap between the lipid bilayers but this time
>>the gap
>>   is not so large as it was in the earlier run (as discussed
>>   earlier in previous email).
>>
>>   As I was already running the NPT equillibration(which I
>>obtained
>>   after the earlier NVT job, which ended in large gap between
>>   layers), i just wanted to observe it and here there is no
>>gap in
>>   between the layers i.e. in npt.gro.
>>
>>   Please suggest me what to do to lower the gap after NVT
>>   equillibration even after applying the lipid restraints
>>and is
>>   it ok for my NPT equillibration as there are no gaps
>>between the
>>   layers after this NPT equillibration.
>>
>>
>>   The gap arises because the lipids (when free to move) are
>>attracted
>>   to the water above and below the bilayer.  If the protein is
>>   restrained, it doesn't move. The box size in NVT is fixed, so
>> the
>>   system is trying to fill it.  It could be that your box was
>>   inappropriately assigned (too large), but maybe not.
>>
>>   I am surprised that, even when using position restraints, the
>>lipids
>>   still separated at all.  Did you use the lipid_posre.itp file
>>that I
>>   provide on the tutorial site?  It has always worked well for
>>me in
>>   such cases.  You could also try increasing the force constant
>>in the
>>   z-dimension.
>>
>>   The other option is to do NPT simulated annealing, as I also
>>suggest
>>   in the troubleshooting page.  Using NPT allows the box to
>>deform in
>>   response to the system, so you will probably get less weird
>>   behavior.  I have found that both NVT with PR and simulated
>>   annealing can get the job done.
>>
>>   -Justin
>>
>>

Re: [gmx-users] Generating a .gro file from .pdb file

[Mark Abraham]

Justin A. Lemkul wrote:



Lum Nforbi wrote:

Hello everyone,
  Thanks to Justin Lemkul and Thomas Schlesier for replying to my 
question in vol. 65 issues 96 and 98.
  I am trying to convert a pdb file to a gro file using pdb2gmx -f 
waters.pdb -o waters.gro and I get the message:


No, that procedure generates a topology file, it is not the correct tool 
for a change of coordinate format (which is almost never needed anyway). 
As a side effect, it regularizes an input coordinate file which might 
have been in one of various formats, and outputs a coordinate file whose 
default format happens to be .gro (but could be a range of 
possibilities). I wish tutorial writers would not give new people the 
wrong impression about the purpose of this step!




Select the Force Field:
 0: GROMOS96 43a1 force field
 1: GROMOS96 43a2 force field (improved alkane dihedrals)
 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 6: [DEPRECATED] Gromacs force field (see manual)
 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
 8: Encad all-atom force field, using scaled-down vacuum charges
 9: Encad all-atom force field, using full solvent charges  
I don't want to use any of these force fields. I want to use the 
charmm27 one. How do I select that? Do I need to modify the code? If 
so, where do I find it?


I believe the CHARMM force fields are in the development version of the 
code (which you can get through git - see the website).  CHARMM will 
officially be supported in version 4.1, I believe.


If your .../share/gromacs/top directory has a range of ffcharmm27.* 
files then you can "add" CHARMM by editing FF.dat by adding a new entry 
and updating the number of entries. It is unsupported before 4.1, however.


  Also, I read in a Spidertoxin tutorial that editconf can be used 
to convert a .pdb file to a .gro file. I tried this but error message 
says: "No velocities found." 


When? Surely not during your editconf conversion?

I know that pdb files generally do not 
have velocities and these velocities can be generated by setting 
genvel=yes in the mdp file. How can a .pdb file contain initial 
velocities?




That's not an error, really.  A .pdb file cannot, by virtue of its 
format, contain velocities.  You have it right that you need "gen_vel = 
yes" to get started, once you've reached grompp.


Pedantically speaking, a .gro-formatted file with zeroes for the 
velocities is also well-formed input for grompp, but you'll likely need 
to equilibrate longer to achieve suitable velocities for your desired 
ensemble. Using gen_vel = yes is much the better approach.


Mark
___
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

Re: [gmx-users] connection to cvs.gromacs.org timed out

[Mark Abraham]

Marc F. Lensink wrote:

I'm trying to do a cvs update on the 3.3 patches branch, but get a
connection time out on cvs.gromacs.org

is there any way I can resolve this?


Probably the release-3-3-patches branch of git is what you should be 
trying to get, these days. See http://www.gromacs.org/Developer_Zone/Git


Mark


(I need to do the update because of the following:

gmx_disre.c: In function 'gmx_disre':
gmx_disre.c:601: error: too few arguments to function 'calc_nsb'

so a single-file patch would be appreciated as well)

cheers,
marc
___
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!
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] Electrostatic energies of aliphatic carbons in G53a6

[Matteus Lindgren]

Hi all.

 

I am performing a study of protein – solvent interaction energies by using
G53a6 protein force field. The electrostatic interaction energies of the
hydrophobic parts of the protein is low, probably due to the small charges
of those groups. 

 

Is it known that the united atom approach of the aliphatic carbons employed
in the G53a6 force field give smaller electrostatic energies than all-atom
force fields for hydrophobic amino acids? After all, the –CHn groups are
assigned a charge of 0 so the interaction energy should not be higher at
least. Is the effect negligible? Any reference to such a study?

 

Thank you 

Matteus

- 

Matteus Lindgren, graduate student
Department of Chemistry, Umeå University 
SE-901 87 Umeå, Sweden
Phone:  +46 (0)90-7865368  

 

 

___
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

RE: [gmx-users] direction_periodic

[Berk Hess]

I am not sure I continued the simulation long enough.
I'll run it again tomorrow.

Berk

> Date: Mon, 28 Sep 2009 16:57:19 +0200
> From: alexander.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] direction_periodic
> 
> Well..they do move forward for a few ps and then they move back (they
> oscillate).
> Did you check for a longer period?
> 
> Alex
> 
> Berk Hess schrieb:
> > Strange...
> > I tested the code on the files you sent me
> > and the slabs were moving smoothly.
> >
> > Berk
> >
> > > Date: Mon, 28 Sep 2009 15:40:16 +0200
> > > From: alexander.h...@mytum.de
> > > To: gmx-users@gromacs.org
> > > Subject: Re: [gmx-users] direction_periodic
> > >
> > > Hey,
> > >
> > > so using the new direction_periodic with some kernels that actually work
> > > and the sources from the git (unmodified)
> > > gives a nice smooth pull force but no actual mean displacement of the
> > > groups to be pulled (on average they just stay where they are,see
> > > attached graph). I'm still trying to pull them into opposite directions
> > > though.
> > >
> > > I'm using this setup:
> > > pull = umbrella
> > > pull_geometry = direction_periodic
> > > pull_ngroups = 1
> > > pull_group0 = DIAM
> > > pull_group1 = DIAM2
> > > pulldim = Y N N
> > > pull_k1 = 1000.0
> > > pull_rate1 = 0.01
> > > pull_vec1 = -1.0 0.0 0.0
> > >
> > > How can I make the two diamond slabs actually move in opposite
> > > directions rather than just oscillating around their
> > > initial positions?
> > >
> > > Thx,
> > > Alex
> > >
> > > Berk Hess schrieb:
> > > > Hi,
> > > >
> > > > Don't use fortran.
> > > > We will get rid of it before the 4.1 release.
> > > >
> > > > Berk
> > > >
> > > > > Date: Mon, 21 Sep 2009 16:17:17 +0200
> > > > > From: alexander.h...@mytum.de
> > > > > To: gmx-users@gromacs.org
> > > > > Subject: Re: [gmx-users] direction_periodic
> > > > >
> > > > > Hey,
> > > > >
> > > > > ok, I checked this. It works ok with the assembly kernels on my
> > local
> > > > > machine, but it fails with fortran kernels
> > > > > on the HPC and on my local machine.
> > > > >
> > > > > Alex
> > > > >
> > > > > Berk Hess schrieb:
> > > > > > Yes.
> > > > > >
> > > > > > Berk
> > > > > >
> > > > > > > Date: Mon, 21 Sep 2009 14:42:43 +0200
> > > > > > > From: alexander.h...@mytum.de
> > > > > > > To: gmx-users@gromacs.org
> > > > > > > Subject: Re: [gmx-users] direction_periodic
> > > > > > >
> > > > > > > With master branch you mean the code I get via
> > > > > > >
> > > > > > > |git clone git://git.gromacs.org/gromacs.git
> > > > > > >
> > > > > > > right?
> > > > > > >
> > > > > > > Alex
> > > > > > > |
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > Berk Hess schrieb:
> > > > > > > > I tested on your system and got good results.
> > > > > > > > There is still a tricky issue: the pull COM is still
> > determined
> > > > > > > > in the "standard" way by summing distances from the pbcatom.
> > > > > > > > Therefore atoms should not change nearest image from he
> > pbcatom.
> > > > > > > > This would result in nasty noise in the pull COM and force.
> > > > > > > >
> > > > > > > > I would suggest that you try to run the master branch and
> > check
> > > > > > > > if that works.
> > > > > > > >
> > > > > > > > Berk
> > > > > > > >
> > > > > > > > > Date: Mon, 21 Sep 2009 14:31:34 +0200
> > > > > > > > > From: alexander.h...@mytum.de
> > > > > > > > > To: gmx-users@gromacs.org
> > > > > > > > > Subject: [gmx-users] direction_periodic
> > > > > > > > >
> > > > > > > > > Hey,
> > > > > > > > >
> > > > > > > > > after some pain of merging the dev branch into our 4.0.5
> > version
> > > > > > I got
> > > > > > > > > the new pull mode "direction_periodic"
> > > > > > > > > running over the weekend. There's some weird rotation of the
> > > > pulled
> > > > > > > > > objects going on and pbc seem weird as well (there are water
> > > > > > molecules
> > > > > > > > > in those positions where I'd expect the periodic image of my
> > > > diamond
> > > > > > > > > slab which leaves the box at one side). I guess you
> > tested the
> > > > > > new pull
> > > > > > > > > mode somehow, so any ideas what's going on here? I'm still
> > > > trying to
> > > > > > > > > perform the same experiment for which I send you the
> > input files
> > > > > > while
> > > > > > > > > ago and for which you kindly implemented the new pull mode.
> > > > > > > > >
> > > > > > > > > Thx for your help,
> > > > > > > > > Alex
> > > > > > > > >
> > > > > > > > > Berk Hess schrieb:
> > > > > > > > > > I have committed a new pull geometry direction_periodic to
> > > > the git
> > > > > > > > > > master branch. It is not documented yet.
> > > > > > > > > > It works the same at direction, but allows distances to be
> > > > larger
> > > > > > > > > > than half the box and does not add the pull force to the
> > > > virial.
> > > > > > > > > >
> > > > > > > > > > Berk
> > > > > > > > > ___
> > > > > > > > > gmx-users mailing li

Re: [gmx-users] direction_periodic

[aherz]

Well..they do move forward for a few ps and then they move back (they
oscillate).
Did you check for a longer period?

Alex

Berk Hess schrieb:
> Strange...
> I tested the code on the files you sent me
> and the slabs were moving smoothly.
>
> Berk
>
> > Date: Mon, 28 Sep 2009 15:40:16 +0200
> > From: alexander.h...@mytum.de
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] direction_periodic
> >
> > Hey,
> >
> > so using the new direction_periodic with some kernels that actually work
> > and the sources from the git (unmodified)
> > gives a nice smooth pull force but no actual mean displacement of the
> > groups to be pulled (on average they just stay where they are,see
> > attached graph). I'm still trying to pull them into opposite directions
> > though.
> >
> > I'm using this setup:
> > pull = umbrella
> > pull_geometry = direction_periodic
> > pull_ngroups = 1
> > pull_group0 = DIAM
> > pull_group1 = DIAM2
> > pulldim = Y N N
> > pull_k1 = 1000.0
> > pull_rate1 = 0.01
> > pull_vec1 = -1.0 0.0 0.0
> >
> > How can I make the two diamond slabs actually move in opposite
> > directions rather than just oscillating around their
> > initial positions?
> >
> > Thx,
> > Alex
> >
> > Berk Hess schrieb:
> > > Hi,
> > >
> > > Don't use fortran.
> > > We will get rid of it before the 4.1 release.
> > >
> > > Berk
> > >
> > > > Date: Mon, 21 Sep 2009 16:17:17 +0200
> > > > From: alexander.h...@mytum.de
> > > > To: gmx-users@gromacs.org
> > > > Subject: Re: [gmx-users] direction_periodic
> > > >
> > > > Hey,
> > > >
> > > > ok, I checked this. It works ok with the assembly kernels on my
> local
> > > > machine, but it fails with fortran kernels
> > > > on the HPC and on my local machine.
> > > >
> > > > Alex
> > > >
> > > > Berk Hess schrieb:
> > > > > Yes.
> > > > >
> > > > > Berk
> > > > >
> > > > > > Date: Mon, 21 Sep 2009 14:42:43 +0200
> > > > > > From: alexander.h...@mytum.de
> > > > > > To: gmx-users@gromacs.org
> > > > > > Subject: Re: [gmx-users] direction_periodic
> > > > > >
> > > > > > With master branch you mean the code I get via
> > > > > >
> > > > > > |git clone git://git.gromacs.org/gromacs.git
> > > > > >
> > > > > > right?
> > > > > >
> > > > > > Alex
> > > > > > |
> > > > > >
> > > > > >
> > > > > >
> > > > > > Berk Hess schrieb:
> > > > > > > I tested on your system and got good results.
> > > > > > > There is still a tricky issue: the pull COM is still
> determined
> > > > > > > in the "standard" way by summing distances from the pbcatom.
> > > > > > > Therefore atoms should not change nearest image from he
> pbcatom.
> > > > > > > This would result in nasty noise in the pull COM and force.
> > > > > > >
> > > > > > > I would suggest that you try to run the master branch and
> check
> > > > > > > if that works.
> > > > > > >
> > > > > > > Berk
> > > > > > >
> > > > > > > > Date: Mon, 21 Sep 2009 14:31:34 +0200
> > > > > > > > From: alexander.h...@mytum.de
> > > > > > > > To: gmx-users@gromacs.org
> > > > > > > > Subject: [gmx-users] direction_periodic
> > > > > > > >
> > > > > > > > Hey,
> > > > > > > >
> > > > > > > > after some pain of merging the dev branch into our 4.0.5
> version
> > > > > I got
> > > > > > > > the new pull mode "direction_periodic"
> > > > > > > > running over the weekend. There's some weird rotation of the
> > > pulled
> > > > > > > > objects going on and pbc seem weird as well (there are water
> > > > > molecules
> > > > > > > > in those positions where I'd expect the periodic image of my
> > > diamond
> > > > > > > > slab which leaves the box at one side). I guess you
> tested the
> > > > > new pull
> > > > > > > > mode somehow, so any ideas what's going on here? I'm still
> > > trying to
> > > > > > > > perform the same experiment for which I send you the
> input files
> > > > > while
> > > > > > > > ago and for which you kindly implemented the new pull mode.
> > > > > > > >
> > > > > > > > Thx for your help,
> > > > > > > > Alex
> > > > > > > >
> > > > > > > > Berk Hess schrieb:
> > > > > > > > > I have committed a new pull geometry direction_periodic to
> > > the git
> > > > > > > > > master branch. It is not documented yet.
> > > > > > > > > It works the same at direction, but allows distances to be
> > > larger
> > > > > > > > > than half the box and does not add the pull force to the
> > > virial.
> > > > > > > > >
> > > > > > > > > Berk
> > > > > > > > ___
> > > > > > > > gmx-users mailing list gmx-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
> > > > > > >
> > > > > > >
> > > > >
> > >
> --

RE: [gmx-users] direction_periodic

[Berk Hess]

Strange...
I tested the code on the files you sent me
and the slabs were moving smoothly.

Berk

> Date: Mon, 28 Sep 2009 15:40:16 +0200
> From: alexander.h...@mytum.de
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] direction_periodic
> 
> Hey,
> 
> so using the new direction_periodic with some kernels that actually work
> and the sources from the git (unmodified)
> gives a nice smooth pull force but no actual mean displacement of the
> groups to be pulled (on average they just stay where they are,see
> attached graph). I'm still trying to pull them into opposite directions
> though.
> 
> I'm using this setup:
> pull= umbrella
> pull_geometry   = direction_periodic
> pull_ngroups = 1
> pull_group0  = DIAM
> pull_group1  = DIAM2
> pulldim = Y N N
> pull_k1  = 1000.0
> pull_rate1   = 0.01
> pull_vec1= -1.0 0.0 0.0
> 
> How can I make the two diamond slabs actually move in opposite
> directions rather than just oscillating around their
> initial positions?
> 
> Thx,
> Alex
> 
> Berk Hess schrieb:
> > Hi,
> >
> > Don't use fortran.
> > We will get rid of it before the 4.1 release.
> >
> > Berk
> >
> > > Date: Mon, 21 Sep 2009 16:17:17 +0200
> > > From: alexander.h...@mytum.de
> > > To: gmx-users@gromacs.org
> > > Subject: Re: [gmx-users] direction_periodic
> > >
> > > Hey,
> > >
> > > ok, I checked this. It works ok with the assembly kernels on my local
> > > machine, but it fails with fortran kernels
> > > on the HPC and on my local machine.
> > >
> > > Alex
> > >
> > > Berk Hess schrieb:
> > > > Yes.
> > > >
> > > > Berk
> > > >
> > > > > Date: Mon, 21 Sep 2009 14:42:43 +0200
> > > > > From: alexander.h...@mytum.de
> > > > > To: gmx-users@gromacs.org
> > > > > Subject: Re: [gmx-users] direction_periodic
> > > > >
> > > > > With master branch you mean the code I get via
> > > > >
> > > > > |git clone git://git.gromacs.org/gromacs.git
> > > > >
> > > > > right?
> > > > >
> > > > > Alex
> > > > > |
> > > > >
> > > > >
> > > > >
> > > > > Berk Hess schrieb:
> > > > > > I tested on your system and got good results.
> > > > > > There is still a tricky issue: the pull COM is still determined
> > > > > > in the "standard" way by summing distances from the pbcatom.
> > > > > > Therefore atoms should not change nearest image from he pbcatom.
> > > > > > This would result in nasty noise in the pull COM and force.
> > > > > >
> > > > > > I would suggest that you try to run the master branch and check
> > > > > > if that works.
> > > > > >
> > > > > > Berk
> > > > > >
> > > > > > > Date: Mon, 21 Sep 2009 14:31:34 +0200
> > > > > > > From: alexander.h...@mytum.de
> > > > > > > To: gmx-users@gromacs.org
> > > > > > > Subject: [gmx-users] direction_periodic
> > > > > > >
> > > > > > > Hey,
> > > > > > >
> > > > > > > after some pain of merging the dev branch into our 4.0.5 version
> > > > I got
> > > > > > > the new pull mode "direction_periodic"
> > > > > > > running over the weekend. There's some weird rotation of the
> > pulled
> > > > > > > objects going on and pbc seem weird as well (there are water
> > > > molecules
> > > > > > > in those positions where I'd expect the periodic image of my
> > diamond
> > > > > > > slab which leaves the box at one side). I guess you tested the
> > > > new pull
> > > > > > > mode somehow, so any ideas what's going on here? I'm still
> > trying to
> > > > > > > perform the same experiment for which I send you the input files
> > > > while
> > > > > > > ago and for which you kindly implemented the new pull mode.
> > > > > > >
> > > > > > > Thx for your help,
> > > > > > > Alex
> > > > > > >
> > > > > > > Berk Hess schrieb:
> > > > > > > > I have committed a new pull geometry direction_periodic to
> > the git
> > > > > > > > master branch. It is not documented yet.
> > > > > > > > It works the same at direction, but allows distances to be
> > larger
> > > > > > > > than half the box and does not add the pull force to the
> > virial.
> > > > > > > >
> > > > > > > > Berk
> > > > > > > ___
> > > > > > > gmx-users mailing list gmx-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
> > > > > >
> > > > > >
> > > >
> > 
> > > > > > Express yourself instantly with MSN Messenger! MSN Messenger
> > > > > > 
> > > > > >
> > > >
> > 
> > > > > >
> > > > > > ___
> > > > > > gmx-users mailin

Re: [gmx-users] Re: Simulation of a protein in a water/DMSO box

[Justin A. Lemkul]

Vitaly V. Chaban wrote:

Justin,

Simeone will insert only "the needed number of waters" but not the
full box. :)  To do so he will use an option "-maxsol XXX" of genbox.



Indeed, but that's not what you posted in the last message.  Just thought I'd 
make sure that was clear.  I had recommended using -maxsol earlier.  In my 
experience, it has been easier to insert one component first using -ci -nmol, 
then making use of -maxsol.


-Justin


Vitaly

On Mon, Sep 28, 2009 at 5:08 PM, Justin A. Lemkul  wrote:


Vitaly V. Chaban wrote:

Hi Simone,

I would advise you to insert the needed number of waters (genbox -cp
conf.gro -cs water.gro -o conf1.gro) and then do the same with DMSO
((genbox -cp conf1.gro -cs dmso.gro -o conf2.gro). Then just
equilibrate.


I doubt that will work.  The first call to genbox there will fill the box
with water, leaving no room for anything else.

-Justin


Vitaly



I need to run a simulation of a protein in a water/DMSO mixture. I can't
quite understand how should I do this... should I normally solvate the
protein with water and then replace a certain number of water molecules
(according to the needed % of DMSO) with DMSO molecules? But in this
case,
how should I do it? Is there a way of replacing solvent molecules with
other
solvent molecules, but of a different type?
I'm sorry but I don't know which procedure to follow.
Thanks in advance




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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_lists/users.php

Re: [gmx-users] Re: Simulation of a protein in a water/DMSO box

[Vitaly V. Chaban]

Justin,

Simeone will insert only "the needed number of waters" but not the
full box. :)  To do so he will use an option "-maxsol XXX" of genbox.

Vitaly

On Mon, Sep 28, 2009 at 5:08 PM, Justin A. Lemkul  wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> Hi Simone,
>>
>> I would advise you to insert the needed number of waters (genbox -cp
>> conf.gro -cs water.gro -o conf1.gro) and then do the same with DMSO
>> ((genbox -cp conf1.gro -cs dmso.gro -o conf2.gro). Then just
>> equilibrate.
>>
>
> I doubt that will work.  The first call to genbox there will fill the box
> with water, leaving no room for anything else.
>
> -Justin
>
>> Vitaly
>>
>>
>>> I need to run a simulation of a protein in a water/DMSO mixture. I can't
>>> quite understand how should I do this... should I normally solvate the
>>> protein with water and then replace a certain number of water molecules
>>> (according to the needed % of DMSO) with DMSO molecules? But in this
>>> case,
>>> how should I do it? Is there a way of replacing solvent molecules with
>>> other
>>> solvent molecules, but of a different type?
>>> I'm sorry but I don't know which procedure to follow.
>>> Thanks in advance
___
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

Re: [gmx-users] Re: Simulation of a protein in a water/DMSO box

[Justin A. Lemkul]

Vitaly V. Chaban wrote:

Hi Simone,

I would advise you to insert the needed number of waters (genbox -cp
conf.gro -cs water.gro -o conf1.gro) and then do the same with DMSO
((genbox -cp conf1.gro -cs dmso.gro -o conf2.gro). Then just
equilibrate.



I doubt that will work.  The first call to genbox there will fill the box with 
water, leaving no room for anything else.


-Justin


Vitaly



I need to run a simulation of a protein in a water/DMSO mixture. I can't
quite understand how should I do this... should I normally solvate the
protein with water and then replace a certain number of water molecules
(according to the needed % of DMSO) with DMSO molecules? But in this case,
how should I do it? Is there a way of replacing solvent molecules with other
solvent molecules, but of a different type?
I'm sorry but I don't know which procedure to follow.
Thanks in advance

___
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



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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_lists/users.php

Re: [gmx-users] direction_periodic

[aherz]

Hey,

so using the new direction_periodic with some kernels that actually work
and the sources from the git (unmodified)
gives a nice smooth pull force but no actual mean displacement of the
groups to be pulled (on average they just stay where they are,see
attached graph). I'm still trying to pull them into opposite directions
though.

I'm using this setup:
pull= umbrella
pull_geometry   = direction_periodic
pull_ngroups = 1
pull_group0  = DIAM
pull_group1  = DIAM2
pulldim = Y N N
pull_k1  = 1000.0
pull_rate1   = 0.01
pull_vec1= -1.0 0.0 0.0

How can I make the two diamond slabs actually move in opposite
directions rather than just oscillating around their
initial positions?

Thx,
Alex

Berk Hess schrieb:
> Hi,
>
> Don't use fortran.
> We will get rid of it before the 4.1 release.
>
> Berk
>
> > Date: Mon, 21 Sep 2009 16:17:17 +0200
> > From: alexander.h...@mytum.de
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] direction_periodic
> >
> > Hey,
> >
> > ok, I checked this. It works ok with the assembly kernels on my local
> > machine, but it fails with fortran kernels
> > on the HPC and on my local machine.
> >
> > Alex
> >
> > Berk Hess schrieb:
> > > Yes.
> > >
> > > Berk
> > >
> > > > Date: Mon, 21 Sep 2009 14:42:43 +0200
> > > > From: alexander.h...@mytum.de
> > > > To: gmx-users@gromacs.org
> > > > Subject: Re: [gmx-users] direction_periodic
> > > >
> > > > With master branch you mean the code I get via
> > > >
> > > > |git clone git://git.gromacs.org/gromacs.git
> > > >
> > > > right?
> > > >
> > > > Alex
> > > > |
> > > >
> > > >
> > > >
> > > > Berk Hess schrieb:
> > > > > I tested on your system and got good results.
> > > > > There is still a tricky issue: the pull COM is still determined
> > > > > in the "standard" way by summing distances from the pbcatom.
> > > > > Therefore atoms should not change nearest image from he pbcatom.
> > > > > This would result in nasty noise in the pull COM and force.
> > > > >
> > > > > I would suggest that you try to run the master branch and check
> > > > > if that works.
> > > > >
> > > > > Berk
> > > > >
> > > > > > Date: Mon, 21 Sep 2009 14:31:34 +0200
> > > > > > From: alexander.h...@mytum.de
> > > > > > To: gmx-users@gromacs.org
> > > > > > Subject: [gmx-users] direction_periodic
> > > > > >
> > > > > > Hey,
> > > > > >
> > > > > > after some pain of merging the dev branch into our 4.0.5 version
> > > I got
> > > > > > the new pull mode "direction_periodic"
> > > > > > running over the weekend. There's some weird rotation of the
> pulled
> > > > > > objects going on and pbc seem weird as well (there are water
> > > molecules
> > > > > > in those positions where I'd expect the periodic image of my
> diamond
> > > > > > slab which leaves the box at one side). I guess you tested the
> > > new pull
> > > > > > mode somehow, so any ideas what's going on here? I'm still
> trying to
> > > > > > perform the same experiment for which I send you the input files
> > > while
> > > > > > ago and for which you kindly implemented the new pull mode.
> > > > > >
> > > > > > Thx for your help,
> > > > > > Alex
> > > > > >
> > > > > > Berk Hess schrieb:
> > > > > > > I have committed a new pull geometry direction_periodic to
> the git
> > > > > > > master branch. It is not documented yet.
> > > > > > > It works the same at direction, but allows distances to be
> larger
> > > > > > > than half the box and does not add the pull force to the
> virial.
> > > > > > >
> > > > > > > Berk
> > > > > > ___
> > > > > > gmx-users mailing list gmx-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
> > > > >
> > > > >
> > >
> 
> > > > > Express yourself instantly with MSN Messenger! MSN Messenger
> > > > > 
> > > > >
> > >
> 
> > > > >
> > > > > ___
> > > > > gmx-users mailing list gmx-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 list gmx-users@gromacs.org
> > > > htt

[gmx-users] Re: Simulation of a protein in a water/DMSO box

[Vitaly V. Chaban]

Hi Simone,

I would advise you to insert the needed number of waters (genbox -cp
conf.gro -cs water.gro -o conf1.gro) and then do the same with DMSO
((genbox -cp conf1.gro -cs dmso.gro -o conf2.gro). Then just
equilibrate.

Vitaly


>
> I need to run a simulation of a protein in a water/DMSO mixture. I can't
> quite understand how should I do this... should I normally solvate the
> protein with water and then replace a certain number of water molecules
> (according to the needed % of DMSO) with DMSO molecules? But in this case,
> how should I do it? Is there a way of replacing solvent molecules with other
> solvent molecules, but of a different type?
> I'm sorry but I don't know which procedure to follow.
> Thanks in advance
___
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] Re: Generating a .gro file from .pdb file

[Vitaly V. Chaban]

Hi,

editconf -f waters.pdb -o conf.pdb

As for CHARMM, you may select the atoms of interest and incorporate to
your topology (see chapter 5 of the manual)
Also maybe some script for the conversion exist, try to search.

Vitaly

>
> Hello everyone,
>  Thanks to Justin Lemkul and Thomas Schlesier for replying to my question
> in vol. 65 issues 96 and 98.
>  I am trying to convert a pdb file to a gro file using pdb2gmx -f
> waters.pdb -o waters.gro and I get the message:
>
> Select the Force Field:
>  0: GROMOS96 43a1 force field
>  1: GROMOS96 43a2 force field (improved alkane dihedrals)
>  2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>  3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>  4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>  5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>  6: [DEPRECATED] Gromacs force field (see manual)
>  7: [DEPRECATED] Gromacs force field with hydrogens for NMR
>  8: Encad all-atom force field, using scaled-down vacuum charges
>  9: Encad all-atom force field, using full solvent charges
>
> I don't want to use any of these force fields. I want to use the charmm27
> one. How do I select that? Do I need to modify the code? If so, where do I
> find it?
>      Also, I read in a Spidertoxin tutorial that editconf can be used to
> convert a .pdb file to a .gro file. I tried this but error message says: "No
> velocities found." I know that pdb files generally do not have velocities
> and these velocities can be generated by setting genvel=yes in the mdp file.
> How can a .pdb file contain initial velocities?
>
___
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] Re: Re: Re: Re: Re: Re: Re: umbrella potential

[Ragnarok sdf]

>
>
>
> > To generate each window I use "trjconv -f
> > original_separation_trajectory.xtc -s topol.tpr -dump
> > time_where_specific_distance_is_found -o
> > frame_where_separation_between_structures_is_x.gro"
> > Once I have the coordinate files regarding this specific distance
> > between my pull groups, I simulate each of them (using the same
> > topol.top file, index.ndx...etc) but with the new md_pull.mdp file I've
> > shown here earlier.
> > Is this wrong for wham analysis?
>
> This should be right, hence my confusion about the histogram.  Are you sure
> there's only one peak?  Have you looked at it with a text editor?  There
> should
> be multiple entries in the file, one for each window that you're
> simulating?
>
> -Justin
>
> > Thank you
>

I've looked at the histogram file and it seems a bit complicated for me to
explain so I've taken the liberty to posting into rapidshare. Plese tell me
if you prefer another way for me to show you the file. Here goes the link:
"http://rapidshare.com/files/286048522/histo.xvg.html";
Thank you
___
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

Re: [gmx-users] nvt.gro

[Justin A. Lemkul]

ram bio wrote:

Dear Justin,

When I used the energy mininized system for NPT annealing with position 
restraints on lipids and there was no separation. So, I think I can 
proceed now to equiliration phase 2 (1-ns NPT equilibration-NPT) and 
then run the Molecular Dynamics for data collection(1ns).What do you 
suggest, is it the right way i am following..as i will be not be using 
NVT equillibration anywhere through out the process.




I think that should be fine.  There is really no prescribed way to do 
equilibration, necessarily.  Everyone has their own method.  If you can 
stabilize the temperature and pressure prior to data collection, then you've 
done enough, in general.  Just be aware that my definition of "data collection" 
simply means that you're remove restraints from anything that was previously 
restrained.  Collecting data for membrane protein systems often occurs after 
10-20 ns (or more), to allow for re-orientation of lipids, which is very slow.


-Justin


Thanks,

Ram


On Fri, Sep 25, 2009 at 11:23 PM, Justin A. Lemkul > wrote:




ram bio wrote:

Dear Justin,

As suggested, i increased the force constant in the Z dimension
from 1000 to 1, and did the NVT equillibration, but still
the gap existed, then i gave the output of nvt equillibration
that is nvt.gro as input for the NPT anneling simulation
(suggested as with position constraints, 1000) and simulated and
here also i had gap .between layers when npt.gro was viewed in VMD.

I have a query that is can I use nvt equllibrated system as
input for NPT simualated annealing or should I use the initial
ionized and minimized system for the NPT annaelated simulation,
as the gap is still persisting...


Use the energy-minimized system as the input into annealing.  I have
no idea why this separation would be happening in this system,
unless the box has been prepared improperly.  I chose the KALP-DPPC
system because it is very robust in everything we've tried to
subject it to.

-Justin

Thanks

Ram


On Thu, Sep 24, 2009 at 4:16 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   ram bio wrote:

   Dear Justin,

   As suggested in the tutorial by you i applied the lipid
position
   restraints, while running the NVT  equillibration, but
after the
   job is finished, when i observed the nvt.gro file in VMD,
still
   there is a gap between the lipid bilayers but this time
the gap
   is not so large as it was in the earlier run (as discussed
   earlier in previous email).

   As I was already running the NPT equillibration(which I
obtained
   after the earlier NVT job, which ended in large gap between
   layers), i just wanted to observe it and here there is no
gap in
   between the layers i.e. in npt.gro.

   Please suggest me what to do to lower the gap after NVT
   equillibration even after applying the lipid restraints
and is
   it ok for my NPT equillibration as there are no gaps
between the
   layers after this NPT equillibration.


   The gap arises because the lipids (when free to move) are
attracted
   to the water above and below the bilayer.  If the protein is
   restrained, it doesn't move. The box size in NVT is fixed, so the
   system is trying to fill it.  It could be that your box was
   inappropriately assigned (too large), but maybe not.

   I am surprised that, even when using position restraints, the
lipids
   still separated at all.  Did you use the lipid_posre.itp file
that I
   provide on the tutorial site?  It has always worked well for
me in
   such cases.  You could also try increasing the force constant
in the
   z-dimension.

   The other option is to do NPT simulated annealing, as I also
suggest
   in the troubleshooting page.  Using NPT allows the box to
deform in
   response to the system, so you will probably get less weird
   behavior.  I have found that both NVT with PR and simulated
   annealing can get the job done.

   -Justin

   Thanks

   Ram


   On Tue, Sep 22, 2009 at 8:25 PM, ram bio
mailto:rmbio...@gmail.com>
   >


   

Re: [gmx-users] nvt.gro

[ram bio]

Dear Justin,

When I used the energy mininized system for NPT annealing with position
restraints on lipids and there was no separation. So, I think I can proceed
now to equiliration phase 2 (1-ns NPT equilibration-NPT) and then run the
Molecular Dynamics for data collection(1ns).What do you suggest, is it the
right way i am following..as i will be not be using NVT equillibration
anywhere through out the process.

Thanks,

Ram


On Fri, Sep 25, 2009 at 11:23 PM, Justin A. Lemkul  wrote:

>
>
> ram bio wrote:
>
>> Dear Justin,
>>
>> As suggested, i increased the force constant in the Z dimension from 1000
>> to 1, and did the NVT equillibration, but still the gap existed, then i
>> gave the output of nvt equillibration that is nvt.gro as input for the NPT
>> anneling simulation (suggested as with position constraints, 1000) and
>> simulated and here also i had gap .between layers when npt.gro was viewed in
>> VMD.
>>
>> I have a query that is can I use nvt equllibrated system as input for NPT
>> simualated annealing or should I use the initial ionized and minimized
>> system for the NPT annaelated simulation, as the gap is still persisting...
>>
>>
> Use the energy-minimized system as the input into annealing.  I have no
> idea why this separation would be happening in this system, unless the box
> has been prepared improperly.  I chose the KALP-DPPC system because it is
> very robust in everything we've tried to subject it to.
>
> -Justin
>
>  Thanks
>>
>> Ram
>>
>> On Thu, Sep 24, 2009 at 4:16 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>ram bio wrote:
>>
>>Dear Justin,
>>
>>As suggested in the tutorial by you i applied the lipid position
>>restraints, while running the NVT  equillibration, but after the
>>job is finished, when i observed the nvt.gro file in VMD, still
>>there is a gap between the lipid bilayers but this time the gap
>>is not so large as it was in the earlier run (as discussed
>>earlier in previous email).
>>
>>As I was already running the NPT equillibration(which I obtained
>>after the earlier NVT job, which ended in large gap between
>>layers), i just wanted to observe it and here there is no gap in
>>between the layers i.e. in npt.gro.
>>
>>Please suggest me what to do to lower the gap after NVT
>>equillibration even after applying the lipid restraints and is
>>it ok for my NPT equillibration as there are no gaps between the
>>layers after this NPT equillibration.
>>
>>
>>The gap arises because the lipids (when free to move) are attracted
>>to the water above and below the bilayer.  If the protein is
>>restrained, it doesn't move. The box size in NVT is fixed, so the
>>system is trying to fill it.  It could be that your box was
>>inappropriately assigned (too large), but maybe not.
>>
>>I am surprised that, even when using position restraints, the lipids
>>still separated at all.  Did you use the lipid_posre.itp file that I
>>provide on the tutorial site?  It has always worked well for me in
>>such cases.  You could also try increasing the force constant in the
>>z-dimension.
>>
>>The other option is to do NPT simulated annealing, as I also suggest
>>in the troubleshooting page.  Using NPT allows the box to deform in
>>response to the system, so you will probably get less weird
>>behavior.  I have found that both NVT with PR and simulated
>>annealing can get the job done.
>>
>>-Justin
>>
>>Thanks
>>
>>Ram
>>
>>
>>On Tue, Sep 22, 2009 at 8:25 PM, ram bio > >>> wrote:
>>
>>   Dear Justin,
>>
>>   Thanks for the suggestion, will try to apply position
>>restraints on
>>   lipid as mentioned in the advanced trouble shooting section.
>>
>>   Ram
>>
>>
>>   On Tue, Sep 22, 2009 at 8:08 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>   >> wrote:
>>
>>
>>
>>   ram bio wrote:
>>
>>   Dear Gromacs Users,
>>
>>   I am following the justin tutorial on KALP-15 in lipid
>>   bilayer, I have a query regarding the nvt.gro that is
>>after
>>   the NVT equillibration phase. The mdrun was proper
>>without
>>   any warnings or errors, but when i visuallized the
>>nvt.gro
>>   in VMD, i found that the peptide is intact in between
>> the
>>   bilayers, but the the two layers got separated or
>>else it is
>>   like the peptide bridging the the two halves of the
>> lipid
>>   bilayer with gap in between the layers and also found
>> few
>>   water molecules to the sides of the p

Re: [gmx-users] Re: Re: Re: Re: Re: Re: umbrella potential

[Justin A. Lemkul]

Stefan Hoorman wrote:

To generate each window I use "trjconv -f 
original_separation_trajectory.xtc -s topol.tpr -dump 
time_where_specific_distance_is_found -o 
frame_where_separation_between_structures_is_x.gro"
Once I have the coordinate files regarding this specific distance 
between my pull groups, I simulate each of them (using the same 
topol.top file, index.ndx...etc) but with the new md_pull.mdp file I've 
shown here earlier.

Is this wrong for wham analysis?


This should be right, hence my confusion about the histogram.  Are you sure 
there's only one peak?  Have you looked at it with a text editor?  There should 
be multiple entries in the file, one for each window that you're simulating?


-Justin


Thank you




___
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


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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_lists/users.php

[gmx-users] Re: Re: Re: Re: Re: Re: umbrella potential

[Stefan Hoorman]

2009/9/28 

>
> Stefan Hoorman wrote:
>
> >
> > Ok. The histogram is the actual result. As I said, my windows are all
> > there, all the reaction coordinates I mentioned before are there to be
> > analysed and in the correct order, but the result comes always the same
> > way. This histogram is the actual result.
>
> Then all your sampling is occurring in one window.  That's your problem.  I
> don't know how you're generating your inputs for the different windows, but
> likely something is going wrong there.
>
> > I will try pulling in only one direction then. Should have the results
> > in a few days.
>
> Probably won't make a difference.  The problem more likely lies in what
> I've
> described above.
>
> -Justin
>
> > Thank you
>

To generate each window I use "trjconv -f original_separation_trajectory.xtc
-s topol.tpr -dump time_where_specific_distance_is_found -o
frame_where_separation_between_structures_is_x.gro"
Once I have the coordinate files regarding this specific distance between my
pull groups, I simulate each of them (using the same topol.top file,
index.ndx...etc) but with the new md_pull.mdp file I've shown here earlier.
Is this wrong for wham analysis?
Thank you
___
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

Re: [gmx-users] Simulation of a protein in a water/DMSO box

[Justin A. Lemkul]

Simone Cirri wrote:

Hi everyone,

I need to run a simulation of a protein in a water/DMSO mixture. I can't 
quite understand how should I do this... should I normally solvate the 
protein with water and then replace a certain number of water molecules 
(according to the needed % of DMSO) with DMSO molecules? But in this 
case, how should I do it? Is there a way of replacing solvent molecules 
with other solvent molecules, but of a different type?

I'm sorry but I don't know which procedure to follow.
Thanks in advance



The easiest way I can think of is to define the box around your protein, use 
genbox -ci -nmol to insert the desired number of DMSO molecules, and then fill 
the box with water.  You may have to tweak the box size or use genbox -maxsol to 
get the desired concentration.


-Justin


Simone Cirri

simoneci...@gmail.com 




___
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


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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_lists/users.php

Re: [gmx-users] Generating a .gro file from .pdb file

[Justin A. Lemkul]

Lum Nforbi wrote:

Hello everyone,
  Thanks to Justin Lemkul and Thomas Schlesier for replying to my 
question in vol. 65 issues 96 and 98.
  I am trying to convert a pdb file to a gro file using pdb2gmx -f 
waters.pdb -o waters.gro and I get the message:


Select the Force Field:
 0: GROMOS96 43a1 force field
 1: GROMOS96 43a2 force field (improved alkane dihedrals)
 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 6: [DEPRECATED] Gromacs force field (see manual)
 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
 8: Encad all-atom force field, using scaled-down vacuum charges
 9: Encad all-atom force field, using full solvent charges   

I don't want to use any of these force fields. I want to use the 
charmm27 one. How do I select that? Do I need to modify the code? If so, 
where do I find it?


I believe the CHARMM force fields are in the development version of the code 
(which you can get through git - see the website).  CHARMM will officially be 
supported in version 4.1, I believe.


  Also, I read in a Spidertoxin tutorial that editconf can be used 
to convert a .pdb file to a .gro file. I tried this but error message 
says: "No velocities found." I know that pdb files generally do not have 
velocities and these velocities can be generated by setting genvel=yes 
in the mdp file. How can a .pdb file contain initial velocities?




That's not an error, really.  A .pdb file cannot, by virtue of its format, 
contain velocities.  You have it right that you need "gen_vel = yes" to get 
started, once you've reached grompp.


-Justin


Thank you,
Lum




___
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


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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_lists/users.php

[gmx-users] Simulation of a protein in a water/DMSO box

[Simone Cirri]

Hi everyone,

I need to run a simulation of a protein in a water/DMSO mixture. I can't
quite understand how should I do this... should I normally solvate the
protein with water and then replace a certain number of water molecules
(according to the needed % of DMSO) with DMSO molecules? But in this case,
how should I do it? Is there a way of replacing solvent molecules with other
solvent molecules, but of a different type?
I'm sorry but I don't know which procedure to follow.
Thanks in advance

Simone Cirri

simoneci...@gmail.com
___
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] Generating a .gro file from .pdb file

[Lum Nforbi]

Hello everyone,
  Thanks to Justin Lemkul and Thomas Schlesier for replying to my question
in vol. 65 issues 96 and 98.
  I am trying to convert a pdb file to a gro file using pdb2gmx -f
waters.pdb -o waters.gro and I get the message:

Select the Force Field:
 0: GROMOS96 43a1 force field
 1: GROMOS96 43a2 force field (improved alkane dihedrals)
 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 6: [DEPRECATED] Gromacs force field (see manual)
 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
 8: Encad all-atom force field, using scaled-down vacuum charges
 9: Encad all-atom force field, using full solvent charges

I don't want to use any of these force fields. I want to use the charmm27
one. How do I select that? Do I need to modify the code? If so, where do I
find it?
  Also, I read in a Spidertoxin tutorial that editconf can be used to
convert a .pdb file to a .gro file. I tried this but error message says: "No
velocities found." I know that pdb files generally do not have velocities
and these velocities can be generated by setting genvel=yes in the mdp file.
How can a .pdb file contain initial velocities?

Thank you,
Lum
___
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

Re: [gmx-users] Static build

[Jack Shultz]

Thanks, I switched to a fedora VM and it built properly.

On Mon, Sep 28, 2009 at 4:26 AM, Ansgar Esztermann  wrote:
>
> On Sep 27, 2009, at 6:24 , Jack Shultz wrote:
>
>> I'm trying to find a package that distributes libSM.a
>
> In case you have trouble finding the correct package: if you are on an
> rpm-bases system (e.g. Redhat, CentOS, SuSE), try
> rpm -qf /usr/bin/libSM.so to find the package providing the shared library.
> The corresponding static lib should be in a package with a similar name, but
> with a -dev or -devel suffix.
>
>
> A.
>
> --
> Ansgar Esztermann
> DV-Systemadministration
> Max-Planck-Institut für biophysikalische Chemie, Abteilung 105
>
> ___
> gmx-users mailing list    gmx-us...@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 thewww interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org
___
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] connection to cvs.gromacs.org timed out

[Marc F. Lensink]

I'm trying to do a cvs update on the 3.3 patches branch, but get a
connection time out on cvs.gromacs.org

is there any way I can resolve this?

(I need to do the update because of the following:

gmx_disre.c: In function 'gmx_disre':
gmx_disre.c:601: error: too few arguments to function 'calc_nsb'

so a single-file patch would be appreciated as well)

cheers,
marc
___
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

Re: [gmx-users] Static build

[Ansgar Esztermann]

On Sep 27, 2009, at 6:24 , Jack Shultz wrote:


I'm trying to find a package that distributes libSM.a


In case you have trouble finding the correct package: if you are on an  
rpm-bases system (e.g. Redhat, CentOS, SuSE), try
rpm -qf /usr/bin/libSM.so to find the package providing the shared  
library. The corresponding static lib should be in a package with a  
similar name, but with a -dev or -devel suffix.



A.

--
Ansgar Esztermann
DV-Systemadministration
Max-Planck-Institut für biophysikalische Chemie, Abteilung 105

___
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] Re: viscosity and acflen in g_energy

[Vitaly V. Chaban]

> Viscosity in g_energy is computed from the pressure tensor which is
> stored in the energy file. Unfortunately is seems like the acflen is
> ignored in this case. Please submit a bugzilla.

Done.

> On the other hand you need all the data you can get for this quantity,
> because it converges extremely slowly.

If the system is quite big and the simul
___
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] Re: viscosity and acflen in g_energy

[Vitaly V. Chaban]

> Viscosity in g_energy is computed from the pressure tensor which is
> stored in the energy file. Unfortunately is seems like the acflen is
> ignored in this case. Please submit a bugzilla.

Done.

> On the other hand you need all the data you can get for this quantity,

If the system is very big but the simulation time isn't such, you are
absolutely true . In other cases it makes a problem... :)
___
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