Re: [gmx-users] Energy Minimization with Lipid Bilayer

[Justin Lemkul]

Hi Tsjerk,

Thanks for helpful advice.  I decided to re-build my system from scratch, and I
ran energy minimization again.  This still ended badly, with a potential energy
on the order of 10^8.  Better than 10^18, but still not anywhere close to
acceptable.

> My guess is that you've generated severe overlaps. On your starting
> structure (the one you use as input to grompp) run trjconv -s in.gro
> -f in.gro -o out.pdb -pbc inbox

The out.pdb shows that some waters that were initially placed below the DPPC
bilayer (crystal waters from the original structure) are now in a thin slab at
the top of my box.  I'm guessing this is a consequence of pbc, although these
were not applied during my minimization steps.  I centered my system in the box
before beginning (edticonf -c), so I don't know how these residues escaped as a
single unit.

Also problematic is that there are water molecules inside the DPPC bilayer, and
I'm wondering how they got there.  Should I just delete these offending
molecules and try to minimize again?

Any thoughts?  Thanks in advance; I've placed my minim.mdp file below this mail
for your reference.  Hopefully I'm not doing anything obviously wrong, I'm
still very new to Gromacs.

-Justin

Justin A. Lemkul
Department of Biochemistry
Virginia Tech

-
minim.mdp

; LINES STARTING WITH ';' ARE COMMENTS
title   = 100-ps minimization of DPPC Bilayer with water box ; Title of 
run

; The following lines tell the program the standard locations where to find
certain files
cpp = /usr/bin/cpp  ; Preprocessor
define  = -DFLEX_SPC
include = -I./  ; Directories to include in the topology format

; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
dt  = 0.002 ; Time step in ps
emtol   = 1000.0; Stop minimization when the maximum force < 
10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to 
perform
xtc_grps= system; Which coordinate group(s) to write to disk
energygrps  = system; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 10; Frequency to update the neighbor list and 
long range forces
ns_type = simple; Method to determine neighbor list (simple, 
grid)
rlist   = 0.9   ; Cut-off for making neighbor list (short range 
forces)
coulombtype = cut-off   ; Treatment of long range electrostatic 
interactions
rcoulomb= 0.9   ; long range electrostatic cut-off
rvdw= 0.9   ; long range Van der Waals cut-off
pbc = no; Periodic Boundary Conditions (yes/no)

; Parameters for temperature and pressure
tau_t   = 0.1
tc-grps = system
ref_t   = 323
tau_p   = 5
ref_p   = 1.0
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] How to get a equilibriumed system effectively

[David van der Spoel]

Qiao Baofu wrote:

Hi all,

Now I meet a problem when building a system.  I used prodrg to get the 
.pdb of a single molecule, write the .top file manually. The 
single-molecule system is equilibriumed (em, NVE, NTV,NTP are all ok for 
at least 1 ns). Then I used  two method  to get a bigger (8 molecules) 
system: 1) genbox -cs -box; 2) genbox -nmol -ci -cp. Both result are ok 
when EM. But when NVE is runn, result 2 crashed right now . For results 
1, NVE is ok, and short-time NTV and NTP(about 10ps) are ok, but 
long-time NTV  and NTP(1ns) crashed with the same reason.


On the other hand, I build a very dilute sytem (5 molecules, density is 
about 2 g/l). It runs very well. But the problem is it is very hard to 
converge to the suitable density (1000 g/l).


Who knows how to solve it? Thanks a lot. 



Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226

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

Variable ci has value -2147483648. It should have been within [ 0 .. 1000 ]
Please report this to the mailing list ( gmx-users@gromacs.org 
)

---


--

Baofu Qiao




___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php
You can scale the system size by coupling to a pressure of e.g. 1000 
bar, use a cutoff rather than PME to speed up this bit. Then, when your 
system is condensed you re-equilibrate with normal pressure coupling and 
PME.


--
David.

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

___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] How to get a equilibriumed system effectively

[Qiao Baofu]

Hi all,

Now I meet a problem when building a system.  I used prodrg to get the .pdb
of a single molecule, write the .top file manually. The single-molecule
system is equilibriumed (em, NVE, NTV,NTP are all ok for at least 1 ns).
Then I used  two method  to get a bigger (8 molecules) system: 1) genbox -cs
-box; 2) genbox -nmol -ci -cp. Both result are ok when EM. But when NVE is
runn, result 2 crashed right now . For results 1, NVE is ok, and short-time
NTV and NTP(about 10ps) are ok, but long-time NTV  and NTP(1ns) crashed with
the same reason.

On the other hand, I build a very dilute sytem (5 molecules, density is
about 2 g/l). It runs very well. But the problem is it is very hard to
converge to the suitable density (1000 g/l).

Who knows how to solve it? Thanks a lot.


Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226

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

Variable ci has value -2147483648. It should have been within [ 0 .. 1000 ]
Please report this to the mailing list (gmx-users@gromacs.org)
---


--

Baofu Qiao
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] g_hbond -contact option

[Yang Ye]

Besides used for h-bond, g_hbond can be used for determine whether the 
distance has fallen into a range (with -nocontact and -r and -r2).


g_dist is not good for calculate for distance between two atoms but 
g_mindist can perform this job well. Actually, because of a compulsive 
input of tpr file, g_dist has less use than g_mindist when coming to 
mere distance calculation.


Regards,
Yang Ye

On 11/22/2006 5:46 PM, andrea carotti wrote:

Hi all,
I have found this interesting option in g_hbond, and I would like to
know something more about it. How does it work? Which is the difference
with other tools like g_dist?
Thanks to all
Andrea

___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

  



___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Re: how to add potassium ions correctly?

[Hu Zhongqiao]

Hi, Mark, thanks for your reply.
 
After some efforts I have been successful to insert potassium using ff
oplsaa. But it seems that ff g43a1 actually can not recognize K or K+.
It doesnt matter, anyway I can select ff oplsaa.
 
Zhongqiao Hu
 
Lab E5-04-27
Tel: 65161946(O)
Department of Chemical and Biomolecular Engineering
National University of Singapore
117576, Singapore
 
 
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] pull code, constraint force

[Chinmay Das]

Hi,
I am trying to calculate free energy and diffusivity of a guest
molecule at a given height from lipid bilayer. I am using pull code
with runtype=constraint, reftype=com, pulldim=N N Y
in version 3.3.1 compiled in double precision. The ensemble is NPT
(Nose-Hoover/ Parrinello-Rahman).

To save on storage, I included extra lines in src/kernel/md.c to
calculate displacements of the guest molecule and force felt by the
guest molecule. This is included just before updating
   xx = (do_per_step(step,inputrec->nstxout) ...

To get the force components, I am summing the force for all atoms in
the molecule - which should cancel out intra-molecule contributions.

The z component of the force is about the same as the output in
pull.pdo - but not quite so. The differences are in the third decimal
place - which is too large for double precision.

Am I missing something and the constraint force is not same as the
force felt by the molecule? Or the difference is because I am
calculating the force at the beginning of the time step, while the
pull code, as far as I can make out, uses iterative scheme to fix the
constraint as part of the updating scheme? Or errors are accumulating
in the iterative scheme?

Finally this is probably not at all important for calculating
diffusion constant (from force auto-correlation) or free-energy
derivative (average z force) because the difference is small - but a
personal curiosity about what is going on and to find out if I am
missing some subtle point.

With best regards
Chinmay
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] (no subject)

[raja]

Hi,

If you want to get it …go here(if you are luck)
http://www.gromacs.org/contributed_by_users/task,cat_view/gid,39/
If you want to make one …go here
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/
If you want to learn how to make then get here 
http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf

If you want to know more on this... search here
http://www.gromacs.org/external/search.html



By,
B.Nataraj



On Wed, 22 Nov 2006 23:33:55 -0800 (PST), "hadi behzadi"
<[EMAIL PROTECTED]> said:
>   Hello, all
>   My question is how can I generate topology file for propanol compound
>   and generate a suitable topology in water solvent.
>
>   thanks a lot
>   
>
>
>
>   Thank a lot foryour guidance.  
>
> 
>  
> -
> Want to start your own business? Learn how on Yahoo! Small Business.
-- 
  raja
  [EMAIL PROTECTED]

-- 
http://www.fastmail.fm - One of many happy users:
  http://www.fastmail.fm/docs/quotes.html

___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Energy Minimization with Lipid Bilayer

[Tsjerk Wassenaar]

Hi Justin,

My guess is that you've generated severe overlaps. On your starting
structure (the one you use as input to grompp) run trjconv -s in.gro
-f in.gro -o out.pdb -pbc inbox
That will map all your atoms to the basic simulation cell. You should
visually inspect the output using your favourite viewer. You're likely
to see all kinds of bonds in the solvent which shouldn't be there,
indicating that you have overlapping residues.


Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  5.9484382e+18
Maximum force =inf on atom 6417
Norm of force =nan


This is s bad. The potential energy should be negative, rather
than around 600 :)

Cheers,

Tsjerk

On 11/22/06, Mark Abraham <[EMAIL PROTECTED]> wrote:

Justin Lemkul wrote:
> Quoting Mark Abraham <[EMAIL PROTECTED]>:
>
>
>>Justin Lemkul wrote:
>>
>>
>>>I also tried running a position-restrained MD (just to see if it might give
>>
>>me
>>
>>>something different), holding the DPPC bilayer fixed and allowing the
>>
>>solvent
>>
>>>to move, but I was again frustrated to see:
>>>
>>>Warning: Only triclinic boxes with the first vector parallel to the x-axis
>>
>>and
>>
>>>the second vector in the xy-plane are supported.
>>> Box (3x3):
>>>Box[0]={ nan,  nan,  nan}
>>>Box[1]={ nan,  nan,  nan}
>>>Box[2]={ nan,  nan,  nan}
>>> Can not fix pbc.
>>>
>>>In the MD, I am applying PBC.  I am wondering if this output is a result of
>>
>>a
>>
>>>poorly minimized starting structure, or if these errors are in any way
>>
>>related?
>>
>>Hmmm in order that we can see what your .gro file is doing, can you
>>please post the results of
>>
>>head -n 10 conf.gro
>>tail -n 10 conf.gro
>>wc -l conf.gro
>
>
> Hopefully this will help:

Unfortunately all seems to be in order there. The second line has the
right number of atoms for the number of lines in the file, and the box
in the final row has the right format.

Can you mail me your .gro, .mdp and .top (and appropriate #included .itp
files) off-list and I'll take a look?

Mark
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
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://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php