Re: [gmx-users] combine two gro into one

[Justin A. Lemkul]

Sikandar Mashayak wrote:
yeah I know its simple, but only concern I have is that, the index of 
atom/residue in two files may not be in agreement, so I have to 
change/shift index of atoms in one of the file.


but anyway I guess I will have to do it manually



That part can be done with genconf -renumber.

-Justin


thanks
sikandar

On Thu, May 13, 2010 at 10:02 PM, Justin A. Lemkul > wrote:




Sikandar Mashayak wrote:

I need to do water channel simulations... I have two gro files
with me...one for wall atoms and one for water atoms...assuming
the co-ordinates of atoms are appropriate, I just need to rename
the indices of each atom appropriately and append one file to
anotherI plan to do it by hand...but it will be great if
there is an automatic way of doing it in gromacs?


This is a simple task that can be done with the Unix 'cat' command.
 Thus there is no Gromacs tool that reproduces this function.  A few
seconds with a text editor after concatenation to remove unnecessary
title lines and box vectors and you're done, assuming (as you've
said) that all the coordinates are appropriately defined.  The whole
process probably takes less typing than sending this email :)

-Justin

thanks
sikandar


-- 



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


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--


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


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Re: [gmx-users] combine two gro into one

[Sikandar Mashayak]

yeah I know its simple, but only concern I have is that, the index of
atom/residue in two files may not be in agreement, so I have to change/shift
index of atoms in one of the file.

but anyway I guess I will have to do it manually

thanks
sikandar

On Thu, May 13, 2010 at 10:02 PM, Justin A. Lemkul  wrote:

>
>
> Sikandar Mashayak wrote:
>
>> I need to do water channel simulations... I have two gro files with
>> me...one for wall atoms and one for water atoms...assuming the co-ordinates
>> of atoms are appropriate, I just need to rename the indices of each atom
>> appropriately and append one file to anotherI plan to do it by
>> hand...but it will be great if there is an automatic way of doing it in
>> gromacs?
>>
>>
> This is a simple task that can be done with the Unix 'cat' command.  Thus
> there is no Gromacs tool that reproduces this function.  A few seconds with
> a text editor after concatenation to remove unnecessary title lines and box
> vectors and you're done, assuming (as you've said) that all the coordinates
> are appropriately defined.  The whole process probably takes less typing
> than sending this email :)
>
> -Justin
>
>  thanks
>> sikandar
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] fep: continuation of run after lambda = 1

[Evelyne Deplazes]

Hi

I am simulating a system consisting of a protein embedded in membrane,
solvated with water using the Martini forcefield. I have set up a free
energy perturbation simulation where a subset of the protein particles are
being converted from their original particle type (state A, lambda =0) to a
new particle type (state B, lambda =1). I have finished a 500 ns run with
the following fep options

free_energy = yes
init_lambda = 0.0
delta_lambda = 5.0e-8

the no. of steps of the simulation is

nsteps  = 2000
dt  = 0.025

hence lambda = 1 after 500ns. so in theory the confout.gro should contain
the structure with all the "fep" particles in state B. I now want to
continue the simulation with the new particle types without any fep options
(ie a simple md run).

I have tried the following to continue my simulation:

1. I used the same *itp file and a new .mdp file with

free_energy = yes
init_lambda = 1.0
delta_lambda = 0.0

gen_vel = 0

I grommp-ed the new .mdp file (using the same *top, *itp and *gro file as
for the original grompp) and continued the run using the state.cpt files
from the end of the 500ns run.

The run crashed with the following msg

--
Step 2022, time 51 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms inf, max inf (between atoms 345 and 346)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
345346   90.00.2700  inf  0.2700
345347   90.00.2700  inf  0.2700
346347   90.00.2700  inf  0.2700
354355   90.00.2650  inf  0.2650
--

Note: atoms 345, 346 and 347 are particles that have been changed to a new
type during the fep run.

2. I made a new .itp file where I changed all the "fep" particles to be of
the new type (ie state B) and removed all fep parameters in the .mdp file. I
"re-grompped" with the confout.gro from the fep run and the new  .itp and
.mdp files.  This should be like a new simulation without any "memory of its
fep past".

The run crashed with the following msg
--
starting mdrun 'MSCL PROTEIN IN MEMBRANE, SOLVATED, WITH IONS'
2000 steps, 50.0 ps.
step 0
step 100, remaining runtime: 0 s
step 200, remaining runtime: 0 s

Step 264, time 6.6 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 4.088986, max 75.397156 (between atoms 455 and 456)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
464465   49.10.2700   0.2669  0.2700
464466   49.40.2700   0.2829  0.2700
455456   90.00.2650  20.2452  0.2650

--

I also tried to simply minimize the confout.gro (ie the structure after the
fep run has finished) but get the following

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 99 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -1.0321324e+06
Maximum force =  4.4505771e+03 on atom 462
Norm of force =  3.2656403e+01


I thought it might be that I am "re-grompping" and starting the simulation
again. So I set up a test run where there is a continuous simulation. Total
simulation time = 200ns and the fep options are set such that lambda reaches
1 after 100 ns. I was hoping the simulation would simply continue with the
new particle type for the remaining 100 ns. But that crashed as well with
similar LINCS warnings.

Has anyone else ever had a similar problem? I have already spent a fair bit
of time on trying to fix it and also talked to people from the Martini group
who are experiences gromacs user.

any ideas are appreciated

Thanks
-- 
Evelyne Deplazes

PhD student
Theoretical Chemistry group
University of Western Australia
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Re: [gmx-users] combine two gro into one

[Justin A. Lemkul]

Sikandar Mashayak wrote:
I need to do water channel simulations... I have two gro files with 
me...one for wall atoms and one for water atoms...assuming the 
co-ordinates of atoms are appropriate, I just need to rename the indices 
of each atom appropriately and append one file to anotherI plan to 
do it by hand...but it will be great if there is an automatic way of 
doing it in gromacs?




This is a simple task that can be done with the Unix 'cat' command.  Thus there 
is no Gromacs tool that reproduces this function.  A few seconds with a text 
editor after concatenation to remove unnecessary title lines and box vectors and 
you're done, assuming (as you've said) that all the coordinates are 
appropriately defined.  The whole process probably takes less typing than 
sending this email :)


-Justin


thanks
sikandar



--


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


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[gmx-users] combine two gro into one

[Sikandar Mashayak]

I need to do water channel simulations... I have two gro files with me...one
for wall atoms and one for water atoms...assuming the co-ordinates of atoms
are appropriate, I just need to rename the indices of each atom
appropriately and append one file to anotherI plan to do it by
hand...but it will be great if there is an automatic way of doing it in
gromacs?

thanks
sikandar
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Re: [gmx-users] luck works but demo fails

[Mark Abraham]

- Original Message -
From: Emily Curtis 
Date: Friday, May 14, 2010 5:12
Subject: [gmx-users] luck works but demo fails
To: gmx-users@gromacs.org

> I think that I finally managed to get gromacs installed correctly.  When I 
> type luck in the command line I get a random phrase.  When I try to run 
> "demo" I get the following error messages:
> 
dyld: Library not loaded: libmkl_intel_lp64.dylib>   Referenced from: 
/Users/emily/gromacsfolder/bin/pdb2gmx>   Reason: image not found> 
> 
> I think that I have sourced the correct folder by typing:   
> 
> source /Users/emily/gromacsfolder/bin/GMXRC> 
> Does anyone have any idea what I could be doing wrong?  Thank you for any 
> help.

Your dynamic linking is not working. Read the MKL documentation pertinent to 
your platform and try again from the configure step. Alternatively, roll your 
own FFTW per the instructions on the GROMACS webpage.

Mark
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Re: [gmx-users] luck works but demo fails

[Justin A. Lemkul]

Emily Curtis wrote:
I think that I finally managed to get gromacs installed correctly.  When 
I type luck in the command line I get a random phrase.  When I try to 
run "demo" I get the following error messages:


dyld: Library not loaded: libmkl_intel_lp64.dylib
  Referenced from: /Users/emily/gromacsfolder/bin/pdb2gmx
  Reason: image not found


I think that I have sourced the correct folder by typing:   


source /Users/emily/gromacsfolder/bin/GMXRC

Does anyone have any idea what I could be doing wrong?  Thank you for 
any help.




Googling this error brings up a ton of forum posts and help info.  Maybe this is 
along the lines of what you need?


http://software.intel.com/en-us/articles/dyld-library-not-loadedlibiomp5dylib/

-Justin

--


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


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[gmx-users] Free energy and and-to-end distances

[Warren Gallin]

Hi,

I am trying to calculate the relative free energy differences of 
conformations of a peptide as a function of end-to-end distance (linear 
distance between N-terminal nitrogen atom to C-terminal carbon atom).

According to the manual pull code should not be used because the two 
atoms being separated are joined by the constraints of the bonds (Section 6.3, 
Limitations).  However, section 6.4 mentions two ways to get around this 
limitation, but I have not been able to get a clear sense of how to implement 
these ideas.

I am looking at a 15 amino acid peptide, I have run a simple 
simulation, and it appears that the closest the ends get are 0.5 nm and the 
farthest apart that they get is 3.5 nm.  So I thought that the approach would 
be to collect a set of  11 conformations from the original simulation with the 
ends at different distances apart (in steps of about 0.3 nm), add a type 2 
constraint to the topology of each with the A state being 0.5 and the B state 
being 3.5, in the run.mdp file for each run set:

free_energy =   yes
init_lambda =   
delta_lambda=   0

and run a 20 ns simulation on each of the 11 systems.

This kind of run, I gather will yield a dgdl.xvg file for each run.

However, in section 6.4 of the manual it says:

When the position of the minimum
or the constraint length is 1 nm more in state B than in state A, the restraint 
or constraint force is
given by dH/dlambda. The distance between the atoms can be changed as a 
function of  and time by
setting delta-lambda in the .mdp file. The results should be identical 
(although not numerically
due to the different implementations) to the results of the pull code with 
umbrella sampling
and constraint pulling. Unlike the pull code, the free energy code can also 
handle atoms that are
connected by constraints.


But I was going to set my constraints at 0.5 and 3.5, so the difference is not 
1 nm, so my numbers will not be useful.

I have been around in circles with this a number of times, and I was wondering 
if anyone could point me at an example of doing this kind of analysis, or else 
perhaps clarify how to generate the equivalent of pullx and pullf files for 
g_wham analysis without using the pull code.

All advice gratefully accepted.

Warren Gallin

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Re: [gmx-users] Simulation explodes (protein-ligand-protein)

[Justin A. Lemkul]

Giovana Bergamini wrote:

Hi!
We have a problem with a protein-ligand-protein simulation. It is a somewhat
large system (approx. 360 amino acid residues with approx. 70 monosaccharides),
that requires a larger box for proper simulation.
We used exclusions (especifically for the problematic atoms) and restrictions
(tested values of 5000, 2000, 1000 - for backbone and for monosaccharides),
both combined and individually, and when they were kept for the entire
simulation, it went just fine. But when these restrictions and exclusions were
removed, the glycan portion, that isn’t connected to any of the proteins
“explodes”.
Any suggestions?



It sounds like the exclusions and restraints are acting as artificial 
stabilizing factors, leading to the conclusion that the underlying system is 
unstable.  Exclusions may or may not be appropriate - some force fields utilize 
intramolecular exclusions.  If you're excluding energy terms between molecules, 
however, that's not appropriate.


You haven't provided much information about how the system was built, what force 
field you're using, the success of energy minimization, .mdp parameters, etc. 
All of that (and possibly more) may be necessary to diagnose what's going on, 
otherwise, the standard reading applies:


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

-Justin


Thank you in advance,

Giovana Bergamini
Faculdade de Farmácia
Grupo de Bioinformatica Estrutural
Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500
Prédio 43431, sala 202
CEP 91500-970, CP 15005, Porto Alegre, RS, Brazil
tel.: +55 51 3308 7770
http://www.cbiot. ufrgs.br/ bioinfo


Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul


--


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


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Re: [gmx-users] genconf and density of system

[Justin A. Lemkul]

Moeed wrote:

Hello,

I intend to generate a stack of molecules with the command line:

genconf -f Hexane.gro -nbox 8 6 4 -o Hexane-STACK.gro


Hexane.gro has box size of 3*3*3 nm3 and I need to have about 7 
molecules per nm^3. So I multiplied 7 by 27 (box size) to get (7*27=)189 
molecuels. What I get from the above command is (-nbox 8 6 4 )192 but 


Are you sure of that density?  If so, your box dimensions give 27 nm^3, implying 
that you'd have to put all 189 hexane molecules in that 3x3x3 box.  Seems a bit 
crowded to me, at least for a molecule of that size.


the system size in getting bigger as well!.  * 24.0  18.0  
12.0 nm^3.*




The only thing that genconf does is build replicates of a system, it does not 
somehow intelligently pack your system together for you, so these dimensions are 
exactly what you would expect: (8*3), (6*3), (4*3).


Could you dear experts guide me how I can reach the system density I 
want. Also to I wanted to know what is best value -dist option. Is it ok 
if I leave the distance between boxes 0 0 0?




I've already told you a bit about the meaning (or lack thereof) in the density 
of the initial configuration.  You could conceivably simulate under a constant 
volume ensemble once you have a suitable configuration, but then I'd argue that 
you're forcing the density to be right and you're not using appropriate 
conditions.


You can leave -dist set to zero, since the molecules are already in some sort of 
box, and the -dist option just adds additional space between them, which is 
probably not necessary.


The easiest method for building your system may simply be to decide on a box 
size, determine the number of molecules that fit in it, and run:


genbox -ci hexane.gro -nmol (whatever) -box (whatever)

If all your molecules can be placed in the box, genbox will do it for you.

-Justin

Thank you, 


Hexane-STACK.gro:

Glycine aRginine prOline Methionine Alanine Cystine Serine
 3840
1HEX C11   1.786   1.639   1.501  0.  0.  0.
1HEXH112   1.881   1.608   1.500  0.  0.  0.
1HEXH123   1.768   1.696   1.421  0.  0.  0.
1HEXH134   1.770   1.692   1.584  0.  0.  0.
1HEX C25   1.693   1.518   1.499  0.  0.  0.
1HEXH216   1.711   1.461   1.579  0.  0.  0.
1HEXH227   1.710   1.465   1.416  0.  0.  0.
1HEX C38   1.547   1.561   1.501  0.  0.  0.
1HEXH319   1.528   1.617   1.420  0.  0.  0.
1HEXH32   10   1.530   1.615   1.584  0.  0.  0.
1HEX C4   11   1.454   1.440   1.500  0.  0.  0.
1HEXH41   12   1.472   1.384   1.581  0.  0.  0.
1HEXH42   13   1.472   1.386   1.418  0.  0.  0.
1HEX C5   14   1.307   1.483   1.501  0.  0.  0.
1HEXH51   15   1.289   1.539   1.420  0.  0.  0.
1HEXH52   16   1.289   1.537   1.583  0.  0.  0.
1HEX C6   17   1.214   1.361   1.500  0.  0.  0.
1HEXH61   18   1.119   1.392   1.501  0.  0.  0.
1HEXH62   19   1.231   1.307   1.418  0.  0.  0.
1HEXH63   20   1.232   1.305   1.581  0.  0.  0.
2HEX C1   21   1.786   1.639   4.501  0.  0.  0.
2HEXH11   22   1.881   1.608   4.500  0.  0.  0.
2HEXH12   23   1.768   1.696   4.421  0.  0.  0.
2HEXH13   24   1.770   1.692   4.584  0.  0.  0.
2HEX C2   25   1.693   1.518   4.499  0.  0.  0.
2HEXH21   26   1.711   1.461   4.579  0.  0.  0.
2HEXH22   27   1.710   1.465   4.416  0.  0.  0.
2HEX C3   28   1.547   1.561   4.501  0.  0.  0.
2HEXH31   29   1.528   1.617   4.420  0.  0.  0.
2HEXH32   30   1.530   1.615   4.584  0.  0.  0.
2HEX C4   31   1.454   1.440   4.500  0.  0.  0.
2HEXH41   32   1.472   1.384   4.581  0.  0.  0.
2HEXH42   33   1.472   1.386   4.418  0.  0.  0.
2HEX C5   34   1.307   1.483   4.501  0.  0.  0.
2HEXH51   35   1.289   1.539   4.420  0.  0.  0.
2HEXH52   36   1.289   1.537   4.583  0.  0.  0.
.
.
.
.
.
192HEX C1 3821  22.786  16.639  10.501  0.  0.  0.
  192HEXH11 3822  22.881  16.608  10.500  0.  0.  0.
  192HEXH12 3823  22.768  16.696  10.421  0.  0.  0.
  192HEXH13 3824  22.770  16.692  10.584  0.  0.  0.
  192HEX C2 3825  22.693  16.518  10.499  0.  0.  0.
  192HEXH21 3826  22.711  16.461  10.579  0.  0.  0.
  192HEXH22 3827  22.710  16.465  10.416  0.  0.  0.
  192HEX C3 3828  22.547  16.561  10.501  0.  

Re: [gmx-users] adding h2po4 to system

[David van der Spoel]

On 5/13/10 8:31 PM, Tiago Barros wrote:

Dear all,

There was a similar thread in the archives, but I could not find the 
solution to my problem from the only reply (nor in the manual).


I've been trying to add 3 h2po4 ions to my system, as these appear to 
be tightly bound to the protein I want to use in my calculations.


I got hold of a h2po4.gro file (from the mailing list archive) and 
used genbox to successfully had 3 h2po4 molecules to the system. My 
idea was to then change the coordinates my hand in other to match the 
position of the 3 PO4 residues from the crystal structure. As I want 
to use the ffG43a1 force field, I made a modified copy (PO4.itp) of 
the h2po4.itp file so that the atomtype "HO" was modified to "H" (as 
in ffG43a1.atp; but this I already found suspicious). I then added 
#include "PO4.itp" right after the #include "ions.itp" and added "PO4  
3" to the end of the .top file.


grompp stops with the error:

---
Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 1379

Fatal error:
Incorrect number of parameters - found 1, expected 2 or 4 for Bond.
---

Is the 'h2po4.itp" file not appropriate to use with the ffG43a1 force 
field?
Since I made the itp file, it probably needs to be updated to new top 
format. If you check the file it has


[ bonds ]
;  aiaj funct   c0   c1
5 1 1 1.637000e-01

so a force constant has to be added.



Is there a more appropriate way to include PO4 residues from crystal 
structures?


Many thanks,

Tiago



--
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David van der Spoel, PhD, Professor of Biology
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
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[gmx-users] adding h2po4 to system

[Tiago Barros]

Dear all,

There was a similar thread in the archives, but I could not find the  
solution to my problem from the only reply (nor in the manual).


I've been trying to add 3 h2po4 ions to my system, as these appear to  
be tightly bound to the protein I want to use in my calculations.


I got hold of a h2po4.gro file (from the mailing list archive) and  
used genbox to successfully had 3 h2po4 molecules to the system. My  
idea was to then change the coordinates my hand in other to match the  
position of the 3 PO4 residues from the crystal structure. As I want  
to use the ffG43a1 force field, I made a modified copy (PO4.itp) of  
the h2po4.itp file so that the atomtype "HO" was modified to "H" (as  
in ffG43a1.atp; but this I already found suspicious). I then added  
#include "PO4.itp" right after the #include "ions.itp" and added "PO4   
3" to the end of the .top file.


grompp stops with the error:

---
Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 1379

Fatal error:
Incorrect number of parameters - found 1, expected 2 or 4 for Bond.
---

Is the 'h2po4.itp" file not appropriate to use with the ffG43a1 force  
field?


Is there a more appropriate way to include PO4 residues from crystal  
structures?


Many thanks,

Tiago
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[gmx-users] genconf and density of system

[Moeed]

Hello,

I intend to generate a stack of molecules with the command line:

genconf -f Hexane.gro -nbox 8 6 4 -o Hexane-STACK.gro

Hexane.gro has box size of 3*3*3 nm3 and I need to have about 7 molecules
per nm^3. So I multiplied 7 by 27 (box size) to get (7*27=)189 molecuels.
What I get from the above command is (-nbox 8 6 4 )192 but the system size
in getting bigger as well!.  * 24.0  18.0  12.0 nm^3.*

Could you dear experts guide me how I can reach the system density I want.
Also to I wanted to know what is best value -dist option. Is it ok if I
leave the distance between boxes 0 0 0?

Thank you,

Hexane-STACK.gro:

Glycine aRginine prOline Methionine Alanine Cystine Serine
 3840
1HEX C11   1.786   1.639   1.501  0.  0.  0.
1HEXH112   1.881   1.608   1.500  0.  0.  0.
1HEXH123   1.768   1.696   1.421  0.  0.  0.
1HEXH134   1.770   1.692   1.584  0.  0.  0.
1HEX C25   1.693   1.518   1.499  0.  0.  0.
1HEXH216   1.711   1.461   1.579  0.  0.  0.
1HEXH227   1.710   1.465   1.416  0.  0.  0.
1HEX C38   1.547   1.561   1.501  0.  0.  0.
1HEXH319   1.528   1.617   1.420  0.  0.  0.
1HEXH32   10   1.530   1.615   1.584  0.  0.  0.
1HEX C4   11   1.454   1.440   1.500  0.  0.  0.
1HEXH41   12   1.472   1.384   1.581  0.  0.  0.
1HEXH42   13   1.472   1.386   1.418  0.  0.  0.
1HEX C5   14   1.307   1.483   1.501  0.  0.  0.
1HEXH51   15   1.289   1.539   1.420  0.  0.  0.
1HEXH52   16   1.289   1.537   1.583  0.  0.  0.
1HEX C6   17   1.214   1.361   1.500  0.  0.  0.
1HEXH61   18   1.119   1.392   1.501  0.  0.  0.
1HEXH62   19   1.231   1.307   1.418  0.  0.  0.
1HEXH63   20   1.232   1.305   1.581  0.  0.  0.
2HEX C1   21   1.786   1.639   4.501  0.  0.  0.
2HEXH11   22   1.881   1.608   4.500  0.  0.  0.
2HEXH12   23   1.768   1.696   4.421  0.  0.  0.
2HEXH13   24   1.770   1.692   4.584  0.  0.  0.
2HEX C2   25   1.693   1.518   4.499  0.  0.  0.
2HEXH21   26   1.711   1.461   4.579  0.  0.  0.
2HEXH22   27   1.710   1.465   4.416  0.  0.  0.
2HEX C3   28   1.547   1.561   4.501  0.  0.  0.
2HEXH31   29   1.528   1.617   4.420  0.  0.  0.
2HEXH32   30   1.530   1.615   4.584  0.  0.  0.
2HEX C4   31   1.454   1.440   4.500  0.  0.  0.
2HEXH41   32   1.472   1.384   4.581  0.  0.  0.
2HEXH42   33   1.472   1.386   4.418  0.  0.  0.
2HEX C5   34   1.307   1.483   4.501  0.  0.  0.
2HEXH51   35   1.289   1.539   4.420  0.  0.  0.
2HEXH52   36   1.289   1.537   4.583  0.  0.  0.
.
.
.
.
.
192HEX C1 3821  22.786  16.639  10.501  0.  0.  0.
  192HEXH11 3822  22.881  16.608  10.500  0.  0.  0.
  192HEXH12 3823  22.768  16.696  10.421  0.  0.  0.
  192HEXH13 3824  22.770  16.692  10.584  0.  0.  0.
  192HEX C2 3825  22.693  16.518  10.499  0.  0.  0.
  192HEXH21 3826  22.711  16.461  10.579  0.  0.  0.
  192HEXH22 3827  22.710  16.465  10.416  0.  0.  0.
  192HEX C3 3828  22.547  16.561  10.501  0.  0.  0.
  192HEXH31 3829  22.528  16.617  10.420  0.  0.  0.
  192HEXH32 3830  22.530  16.615  10.584  0.  0.  0.
  192HEX C4 3831  22.454  16.440  10.500  0.  0.  0.
  192HEXH41 3832  22.472  16.384  10.581  0.  0.  0.
  192HEXH42 3833  22.472  16.386  10.418  0.  0.  0.
  192HEX C5 3834  22.307  16.483  10.501  0.  0.  0.
  192HEXH51 3835  22.289  16.539  10.420  0.  0.  0.
  192HEXH52 3836  22.289  16.537  10.583  0.  0.  0.
  192HEX C6 3837  22.214  16.361  10.500  0.  0.  0.
  192HEXH61 3838  22.119  16.392  10.501  0.  0.  0.
  192HEXH62 3839  22.231  16.307  10.418  0.  0.  0.
  192HEXH63 3840  22.232  16.305  10.581  0.  0.  0.
 * 24.0  18.0  12.0*



***Hexane.gro
20
> 1HEX C11   1.786   1.639   1.501
> 1HEXH112   1.881   1.608   1.500
> 1HEXH123   1.768   1.696   1.421
> 1HEXH134   1.770   1.692   1.584
> 1HEX C25   1.693   1.518   1.499
> 1HEXH216   1.711   1.461   1.579
> 1HEXH227   1.710   1.465   1.416
> 1HEX C38   

[gmx-users] luck works but demo fails

[Emily Curtis]

I think that I finally managed to get gromacs installed correctly.  When I
type luck in the command line I get a random phrase.  When I try to run
"demo" I get the following error messages:

dyld: Library not loaded: libmkl_intel_lp64.dylib
  Referenced from: /Users/emily/gromacsfolder/bin/pdb2gmx
  Reason: image not found


I think that I have sourced the correct folder by typing:

source /Users/emily/gromacsfolder/bin/GMXRC

Does anyone have any idea what I could be doing wrong?  Thank you for any
help.
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[gmx-users] Simulation explodes (protein-ligand-protein)

[Giovana Bergamini]

Hi!
We have a problem with a protein-ligand-protein simulation. It is a somewhat
large system (approx. 360 amino acid residues with approx. 70 monosaccharides),
that requires a larger box for proper simulation.
We used exclusions (especifically for the problematic atoms) and restrictions
(tested values of 5000, 2000, 1000 - for backbone and for monosaccharides),
both combined and individually, and when they were kept for the entire
simulation, it went just fine. But when these restrictions and exclusions were
removed, the glycan portion, that isn’t connected to any of the proteins
“explodes”.
Any suggestions?

Thank you in advance,

Giovana Bergamini
Faculdade de Farmácia
Grupo de Bioinformatica Estrutural
Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9500
Prédio 43431, sala 202
CEP 91500-970, CP 15005, Porto Alegre, RS, Brazil
tel.: +55 51 3308 7770
http://www.cbiot. ufrgs.br/ bioinfo


Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul
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Re: [gmx-users] g_spatial

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello,
I am trying to calculate spatial distribution function (SDF) for my system.
I have defined the residue name of solute (its glucose, one glucose
molecule) and solvent (its cations of ionic liquids, 128 cations) by group
numbers.
During the g_spatial calculation can I select this group numbers to define
solute and solvent?



Have you actually tried running g_spatial?  I even told you yesterday what 
groups to select for the calculation:


http://lists.gromacs.org/pipermail/gmx-users/2010-May/050879.html

If you want free help, please at least demonstrate that you've paid attention to 
the information you've already been given.  I also updated the wiki page for 
g_spatial to provide some additional information, I'd suggest you check it out 
if you're still having difficulties.


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

-Justin



Thanks

Nilesh









--


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


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[gmx-users] g_spatial

[Nilesh Dhumal]

Hello,
I am trying to calculate spatial distribution function (SDF) for my system.
I have defined the residue name of solute (its glucose, one glucose
molecule) and solvent (its cations of ionic liquids, 128 cations) by group
numbers.
During the g_spatial calculation can I select this group numbers to define
solute and solvent?


Thanks

Nilesh







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[gmx-users] Re: gmx-users Digest, Vol 73, Issue 79

[Anna Duncan]

Thanks for that.  It would have taken me ages to spot the quotation  
marks error...

Everything working fine now, of course...

On 13 May 2010, at 14:58, gmx-users-requ...@gromacs.org wrote:


Re: Use of restraints gives segmentation fault


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[gmx-users] about SHAKE, SETTLE, LINCS and double x single precision

[Alan]

Hi there,

>From what I've read and known, here in the list as well, one of the main
reasons why Gromacs run in single precision is because it has LINCS, besides
SHAKE, which I believe requires double precision for accuracy.

I am drawing such conclusion (that can be wrong) partially based on

Lippert, R. A., Bowers, K. J., Dror, R. O., Eastwood, M. P., Gregersen, B.
A., Klepeis, J. L., Kolossvary, I., and Shaw, D. E. A common, avoidable
source of error in molecular dynamics integrators. Journal of Chemical
Physics 126, 4 (Jan. 2007), 046101–1–046101–2

However, in this letter article they didn't test with LINCS. I would love to
hear some comments from Gromacs developers.

When I started in MD, developing our own MD software, all was done in double
precision, then came Gromacs blowing up this paradigm. (I am aware that even
in Gromacs, there are routines that really requires double precision, e.g.
normal mode analysis).

Essentially I would like to understand better this double x single approach
in MD re accuracy.

Thanks,

Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Re: [gmx-users] Use of restraints gives segmentation fault

[XAvier Periole]

On May 13, 2010, at 3:58 PM, XAvier Periole wrote:



Why don't you simply define a extra bond between your two CYS side  
chains beads?

Sorry, I red to quick ...



On May 13, 2010, at 3:31 PM, Anna Duncan wrote:



I'm trying to energy minimise a protein structure.  In one area of  
the structure there are some salt bridges and when I do an energy  
minimisation without any restraints these are disrupted, which is  
something I want to avoid.  To that end, I've tried restraining the  
residues that are involved, first with position restraints and then  
with distance restraints, but in both cases I get a segmentation  
fault in the same place.

The command I issue looks like:
grompp -f em.mdp -c 1okc_ex.cg.gro -p 1okc_ex.top -o 1okc_min_sbRes  
-v -n salt_bridges.ndx


and the output:
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained_start' by 'continuation'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10#
checking input for internal consistency...

NOTE 1 [file em.mdp, line unknown]:
  For energy conservation with switch/shift potentials, rlist  
should be 0.1

  to 0.3 nm larger than rcoulomb.


NOTE 2 [file em.mdp, line unknown]:
  For energy conservation with switch/shift potentials, rlist  
should be 0.1

  to 0.3 nm larger than rvdw.

processing topology...
Generated 0 of the 465 non-bonded parameter combinations
Segmentation fault

--

Like I say, when I do this without the restraints, grompp and mdrun  
run fine.  The only differences, then, between the input is the  
line in em.mdp:

define = -DDISTRESB

The topoolgy file, 1okc_ex.top looks like:
#include "martini_v2.1.itp"
#include "1okc_ex.itp"
#ifdef POSRESB
#include posre_saltbridges.itp
#endif
#ifdef DISTRESB
#include distre_sb.itp
#endif

[ system ]
1OKC_EX SIMULATION

[ molecules ]
Protein 1

--

The position restraints file looks like:
; position restraints for r_28_r_31_r_133_r_136_r_230_r_233 of God  
Rules Over Mankind, Animals, Cosmos and Such


[ position_restraints ]
;  i funct   fcxfcyfcz
  521   1000   1000   1000
  531   1000   1000   1000
  591   1000   1000   1000
  601   1000   1000   1000
  611   1000   1000   1000
 2961   1000   1000   1000
 2971   1000   1000   1000
 3031   1000   1000   1000
 3041   1000   1000   1000
 3051   1000   1000   1000
 5051   1000   1000   1000
 5061   1000   1000   1000
 5111   1000   1000   1000
 5121   1000   1000   1000
 5131   1000   1000   1000

--

and the distance restraints file looks like:
; distance restraints for h1-h3_sb of God Rules Over Mankind,  
Animals, Cosmos and Such


[ distance_restraints ]
;   i j ? label  funct loup1up2  
weight
   53   395 1 0  12.001812.20181 
3.20181  1
  297   513 1 0  1   0.462702   0.662702  
1.6627  1
   61   506 1 0  1 0.3818 0.5818  
1.5818  1


--


I can't work out what is giving the segmentation fault because I  
think the restraint files are in the right format and I can't think  
of what else would go wrong at this stage for a segmentation fault  
to occur.


In the grompp run that works (without any restraints) the line  
after where the segmentation error occurs in the other cases looks  
like:

Excluding 1 bonded neighbours molecule type 'Protein'

Many thanks,
Anna

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Re: [gmx-users] Use of restraints gives segmentation fault

[XAvier Periole]

Why don't you simply define a extra bond between your two CYS side  
chains beads?


On May 13, 2010, at 3:31 PM, Anna Duncan wrote:



I'm trying to energy minimise a protein structure.  In one area of  
the structure there are some salt bridges and when I do an energy  
minimisation without any restraints these are disrupted, which is  
something I want to avoid.  To that end, I've tried restraining the  
residues that are involved, first with position restraints and then  
with distance restraints, but in both cases I get a segmentation  
fault in the same place.

The command I issue looks like:
grompp -f em.mdp -c 1okc_ex.cg.gro -p 1okc_ex.top -o 1okc_min_sbRes - 
v -n salt_bridges.ndx


and the output:
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained_start' by 'continuation'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10#
checking input for internal consistency...

NOTE 1 [file em.mdp, line unknown]:
  For energy conservation with switch/shift potentials, rlist should  
be 0.1

  to 0.3 nm larger than rcoulomb.


NOTE 2 [file em.mdp, line unknown]:
  For energy conservation with switch/shift potentials, rlist should  
be 0.1

  to 0.3 nm larger than rvdw.

processing topology...
Generated 0 of the 465 non-bonded parameter combinations
Segmentation fault

--

Like I say, when I do this without the restraints, grompp and mdrun  
run fine.  The only differences, then, between the input is the line  
in em.mdp:

define = -DDISTRESB

The topoolgy file, 1okc_ex.top looks like:
#include "martini_v2.1.itp"
#include "1okc_ex.itp"
#ifdef POSRESB
#include posre_saltbridges.itp
#endif
#ifdef DISTRESB
#include distre_sb.itp
#endif

[ system ]
1OKC_EX SIMULATION

[ molecules ]
Protein 1

--

The position restraints file looks like:
; position restraints for r_28_r_31_r_133_r_136_r_230_r_233 of God  
Rules Over Mankind, Animals, Cosmos and Such


[ position_restraints ]
;  i funct   fcxfcyfcz
  521   1000   1000   1000
  531   1000   1000   1000
  591   1000   1000   1000
  601   1000   1000   1000
  611   1000   1000   1000
 2961   1000   1000   1000
 2971   1000   1000   1000
 3031   1000   1000   1000
 3041   1000   1000   1000
 3051   1000   1000   1000
 5051   1000   1000   1000
 5061   1000   1000   1000
 5111   1000   1000   1000
 5121   1000   1000   1000
 5131   1000   1000   1000

--

and the distance restraints file looks like:
; distance restraints for h1-h3_sb of God Rules Over Mankind,  
Animals, Cosmos and Such


[ distance_restraints ]
;   i j ? label  funct loup1up2  
weight
   53   395 1 0  12.001812.20181 
3.20181  1
  297   513 1 0  1   0.462702   0.662702  
1.6627  1
   61   506 1 0  1 0.3818 0.5818  
1.5818  1


--


I can't work out what is giving the segmentation fault because I  
think the restraint files are in the right format and I can't think  
of what else would go wrong at this stage for a segmentation fault  
to occur.


In the grompp run that works (without any restraints) the line after  
where the segmentation error occurs in the other cases looks like:

Excluding 1 bonded neighbours molecule type 'Protein'

Many thanks,
Anna

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Re: [gmx-users] Use of restraints gives segmentation fault

[Justin A. Lemkul]

Anna Duncan wrote:


I'm trying to energy minimise a protein structure.  In one area of the 
structure there are some salt bridges and when I do an energy 
minimisation without any restraints these are disrupted, which is 
something I want to avoid.  To that end, I've tried restraining the 
residues that are involved, first with position restraints and then with 
distance restraints, but in both cases I get a segmentation fault in the 
same place.

The command I issue looks like:
grompp -f em.mdp -c 1okc_ex.cg.gro -p 1okc_ex.top -o 1okc_min_sbRes -v 
-n salt_bridges.ndx


and the output:
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained_start' by 'continuation'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10#
checking input for internal consistency...

NOTE 1 [file em.mdp, line unknown]:
  For energy conservation with switch/shift potentials, rlist should be 0.1
  to 0.3 nm larger than rcoulomb.


NOTE 2 [file em.mdp, line unknown]:
  For energy conservation with switch/shift potentials, rlist should be 0.1
  to 0.3 nm larger than rvdw.

processing topology...
Generated 0 of the 465 non-bonded parameter combinations
Segmentation fault

--

Like I say, when I do this without the restraints, grompp and mdrun run 
fine.  The only differences, then, between the input is the line in em.mdp:

define = -DDISTRESB

The topoolgy file, 1okc_ex.top looks like:
#include "martini_v2.1.itp"
#include "1okc_ex.itp"
#ifdef POSRESB
#include posre_saltbridges.itp
#endif
#ifdef DISTRESB
#include distre_sb.itp
#endif



You have the wrong syntax.  You need " " around your .itp files in the #include 
statements.  Note how your first two #includes look different from your last two :)


-Justin


[ system ]
1OKC_EX SIMULATION

[ molecules ]
Protein 1

--

The position restraints file looks like: 
; position restraints for r_28_r_31_r_133_r_136_r_230_r_233 of God Rules 
Over Mankind, Animals, Cosmos and Such


[ position_restraints ]
;  i funct   fcxfcyfcz
  521   1000   1000   1000
  531   1000   1000   1000
  591   1000   1000   1000
  601   1000   1000   1000
  611   1000   1000   1000
 2961   1000   1000   1000
 2971   1000   1000   1000
 3031   1000   1000   1000
 3041   1000   1000   1000
 3051   1000   1000   1000
 5051   1000   1000   1000
 5061   1000   1000   1000
 5111   1000   1000   1000
 5121   1000   1000   1000
 5131   1000   1000   1000

--

and the distance restraints file looks like:
; distance restraints for h1-h3_sb of God Rules Over Mankind, Animals, 
Cosmos and Such


[ distance_restraints ]
;   i j ? label  funct loup1up2 weight
   53   395 1 0  12.001812.201813.20181  1
  297   513 1 0  1   0.462702   0.662702 1.6627  1
   61   506 1 0  1 0.3818 0.5818 1.5818  1

--


I can't work out what is giving the segmentation fault because I think 
the restraint files are in the right format and I can't think of what 
else would go wrong at this stage for a segmentation fault to occur.


In the grompp run that works (without any restraints) the line after 
where the segmentation error occurs in the other cases looks like:

Excluding 1 bonded neighbours molecule type 'Protein'

Many thanks,
Anna



--


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


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[gmx-users] Use of restraints gives segmentation fault

[Anna Duncan]

I'm trying to energy minimise a protein structure.  In one area of the  
structure there are some salt bridges and when I do an energy  
minimisation without any restraints these are disrupted, which is  
something I want to avoid.  To that end, I've tried restraining the  
residues that are involved, first with position restraints and then  
with distance restraints, but in both cases I get a segmentation fault  
in the same place.

The command I issue looks like:
grompp -f em.mdp -c 1okc_ex.cg.gro -p 1okc_ex.top -o 1okc_min_sbRes -v  
-n salt_bridges.ndx


and the output:
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Replacing old mdp entry 'unconstrained_start' by 'continuation'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10#
checking input for internal consistency...

NOTE 1 [file em.mdp, line unknown]:
  For energy conservation with switch/shift potentials, rlist should  
be 0.1

  to 0.3 nm larger than rcoulomb.


NOTE 2 [file em.mdp, line unknown]:
  For energy conservation with switch/shift potentials, rlist should  
be 0.1

  to 0.3 nm larger than rvdw.

processing topology...
Generated 0 of the 465 non-bonded parameter combinations
Segmentation fault

--

Like I say, when I do this without the restraints, grompp and mdrun  
run fine.  The only differences, then, between the input is the line  
in em.mdp:

define = -DDISTRESB

The topoolgy file, 1okc_ex.top looks like:
#include "martini_v2.1.itp"
#include "1okc_ex.itp"
#ifdef POSRESB
#include posre_saltbridges.itp
#endif
#ifdef DISTRESB
#include distre_sb.itp
#endif

[ system ]
1OKC_EX SIMULATION

[ molecules ]
Protein 1

--

The position restraints file looks like:
; position restraints for r_28_r_31_r_133_r_136_r_230_r_233 of God  
Rules Over Mankind, Animals, Cosmos and Such


[ position_restraints ]
;  i funct   fcxfcyfcz
  521   1000   1000   1000
  531   1000   1000   1000
  591   1000   1000   1000
  601   1000   1000   1000
  611   1000   1000   1000
 2961   1000   1000   1000
 2971   1000   1000   1000
 3031   1000   1000   1000
 3041   1000   1000   1000
 3051   1000   1000   1000
 5051   1000   1000   1000
 5061   1000   1000   1000
 5111   1000   1000   1000
 5121   1000   1000   1000
 5131   1000   1000   1000

--

and the distance restraints file looks like:
; distance restraints for h1-h3_sb of God Rules Over Mankind, Animals,  
Cosmos and Such


[ distance_restraints ]
;   i j ? label  funct loup1up2  
weight
   53   395 1 0  12.001812.20181 
3.20181  1
  297   513 1 0  1   0.462702   0.662702  
1.6627  1
   61   506 1 0  1 0.3818 0.5818  
1.5818  1


--


I can't work out what is giving the segmentation fault because I think  
the restraint files are in the right format and I can't think of what  
else would go wrong at this stage for a segmentation fault to occur.


In the grompp run that works (without any restraints) the line after  
where the segmentation error occurs in the other cases looks like:

Excluding 1 bonded neighbours molecule type 'Protein'

Many thanks,
Anna

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Re: [gmx-users] rerun trajectory does not match input file

[Justin A. Lemkul]

John Shultz wrote:

Thank you Justin, is there a way I can choose both Protein LIG? It has
the following options for me



You need to make a custom group that merges these two.

-Justin


Reading toplogy and shit from md.tpr
Reading file md.tpr, VERSION 4.0.5 (single precision)
5 steps (100 ps) remaining from first run.
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Group 0 (  System) has 37770 elements
Group 1 ( Protein) has  3848 elements
Group 2 (   Protein-H) has  1980 elements
Group 3 ( C-alpha) has   244 elements
Group 4 (Backbone) has   732 elements
Group 5 (   MainChain) has   974 elements
Group 6 (MainChain+Cb) has  1206 elements
Group 7 ( MainChain+H) has  1198 elements
Group 8 (   SideChain) has  2650 elements
Group 9 ( SideChain-H) has  1006 elements
Group10 ( Prot-Masses) has  3848 elements
Group11 ( Non-Protein) has 33922 elements
Group12 ( LIG) has35 elements
Group13 ( SOL) has 33807 elements
Group14 (  Na) has46 elements
Group15 (  Cl) has34 elements
Group16 (   Other) has 33922 elements
Select a group:


On Thu, May 13, 2010 at 9:02 AM, Justin A. Lemkul  wrote:


John Shultz wrote:

I am trying to rerun a simulation using this command
mdrun -rerun -v -deffnm md

I think I must have made a mistake when I prepared the original mdp
file because I get this message
Number of atoms in trajectory (3883) does not match the run input file
(37770)

I have these files in my directory
Complex.top  ener.edr  job.xml  md.cpt  md.edr  md.gro  md.log  md.mdp
 md_prev.cpt  md.tpr  md.trr  md.xtc  traj.trr

Here is my mdp file, should I remove entries for xtc_grps and
energygrps to avoid this issue?


You can, but it won't fix anything.  Your original .xtc file saved only the
coordinates of the Protein and LIG (per your output options), but your .tpr
file has all of these atoms, regardless of what you choose to save.  You
can, however, create a .tpr file that has a just these atoms by passing your
original .tpr file to tpbconv, using a suitable index group.

-Justin


integrator = md
nsteps = 5
dt = 0.002
nstvout = 5000
nstlog = 500
nstenergy = 250
nstxtcout = 5000
nstxout = 5000
xtc_grps = Protein LIG
energygrps = Protein  SOL
constraints = all-bonds
nstcomm = 1
ns_type = grid
rlist = 1.2
rcoulomb = 1.1
rvdw = 1.0
vdwtype = shift
rvdw-switch = 0.9
coulombtype = PME-Switch
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 300 300
Pcoupl = parrinello-rahman
PcOupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
lincs-iter = 2
DispCorr = EnerPres
optimize_fft = yes
gen_seed = 805087

--


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


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--


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


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Re: [gmx-users] rerun trajectory does not match input file

[John Shultz]

Thank you Justin, is there a way I can choose both Protein LIG? It has
the following options for me

Reading toplogy and shit from md.tpr
Reading file md.tpr, VERSION 4.0.5 (single precision)
5 steps (100 ps) remaining from first run.
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Group 0 (  System) has 37770 elements
Group 1 ( Protein) has  3848 elements
Group 2 (   Protein-H) has  1980 elements
Group 3 ( C-alpha) has   244 elements
Group 4 (Backbone) has   732 elements
Group 5 (   MainChain) has   974 elements
Group 6 (MainChain+Cb) has  1206 elements
Group 7 ( MainChain+H) has  1198 elements
Group 8 (   SideChain) has  2650 elements
Group 9 ( SideChain-H) has  1006 elements
Group10 ( Prot-Masses) has  3848 elements
Group11 ( Non-Protein) has 33922 elements
Group12 ( LIG) has35 elements
Group13 ( SOL) has 33807 elements
Group14 (  Na) has46 elements
Group15 (  Cl) has34 elements
Group16 (   Other) has 33922 elements
Select a group:


On Thu, May 13, 2010 at 9:02 AM, Justin A. Lemkul  wrote:
>
>
> John Shultz wrote:
>>
>> I am trying to rerun a simulation using this command
>> mdrun -rerun -v -deffnm md
>>
>> I think I must have made a mistake when I prepared the original mdp
>> file because I get this message
>> Number of atoms in trajectory (3883) does not match the run input file
>> (37770)
>>
>> I have these files in my directory
>> Complex.top  ener.edr  job.xml  md.cpt  md.edr  md.gro  md.log  md.mdp
>>  md_prev.cpt  md.tpr  md.trr  md.xtc  traj.trr
>>
>> Here is my mdp file, should I remove entries for xtc_grps and
>> energygrps to avoid this issue?
>>
>
> You can, but it won't fix anything.  Your original .xtc file saved only the
> coordinates of the Protein and LIG (per your output options), but your .tpr
> file has all of these atoms, regardless of what you choose to save.  You
> can, however, create a .tpr file that has a just these atoms by passing your
> original .tpr file to tpbconv, using a suitable index group.
>
> -Justin
>
>> integrator = md
>> nsteps = 5
>> dt = 0.002
>> nstvout = 5000
>> nstlog = 500
>> nstenergy = 250
>> nstxtcout = 5000
>> nstxout = 5000
>> xtc_grps = Protein LIG
>> energygrps = Protein  SOL
>> constraints = all-bonds
>> nstcomm = 1
>> ns_type = grid
>> rlist = 1.2
>> rcoulomb = 1.1
>> rvdw = 1.0
>> vdwtype = shift
>> rvdw-switch = 0.9
>> coulombtype = PME-Switch
>> Tcoupl = v-rescale
>> tau_t = 0.1 0.1
>> tc-grps = protein non-protein
>> ref_t = 300 300
>> Pcoupl = parrinello-rahman
>> PcOupltype = isotropic
>> tau_p = 0.5
>> compressibility = 4.5e-5
>> ref_p = 1.0
>> gen_vel = yes
>> lincs-iter = 2
>> DispCorr = EnerPres
>> optimize_fft = yes
>> gen_seed = 805087
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing 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!
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> or send it to gmx-users-requ...@gromacs.org.
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>
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Re: [gmx-users] rerun trajectory does not match input file

[Justin A. Lemkul]

John Shultz wrote:

I am trying to rerun a simulation using this command
mdrun -rerun -v -deffnm md

I think I must have made a mistake when I prepared the original mdp
file because I get this message
Number of atoms in trajectory (3883) does not match the run input file (37770)

I have these files in my directory
Complex.top  ener.edr  job.xml  md.cpt  md.edr  md.gro  md.log  md.mdp
 md_prev.cpt  md.tpr  md.trr  md.xtc  traj.trr

Here is my mdp file, should I remove entries for xtc_grps and
energygrps to avoid this issue?



You can, but it won't fix anything.  Your original .xtc file saved only the 
coordinates of the Protein and LIG (per your output options), but your .tpr file 
has all of these atoms, regardless of what you choose to save.  You can, 
however, create a .tpr file that has a just these atoms by passing your original 
.tpr file to tpbconv, using a suitable index group.


-Justin


integrator = md
nsteps = 5
dt = 0.002
nstvout = 5000
nstlog = 500
nstenergy = 250
nstxtcout = 5000
nstxout = 5000
xtc_grps = Protein LIG
energygrps = Protein  SOL
constraints = all-bonds
nstcomm = 1
ns_type = grid
rlist = 1.2
rcoulomb = 1.1
rvdw = 1.0
vdwtype = shift
rvdw-switch = 0.9
coulombtype = PME-Switch
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 300 300
Pcoupl = parrinello-rahman
PcOupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
lincs-iter = 2
DispCorr = EnerPres
optimize_fft = yes
gen_seed = 805087


--


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


--
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[gmx-users] rerun trajectory does not match input file

[John Shultz]

I am trying to rerun a simulation using this command
mdrun -rerun -v -deffnm md

I think I must have made a mistake when I prepared the original mdp
file because I get this message
Number of atoms in trajectory (3883) does not match the run input file (37770)

I have these files in my directory
Complex.top  ener.edr  job.xml  md.cpt  md.edr  md.gro  md.log  md.mdp
 md_prev.cpt  md.tpr  md.trr  md.xtc  traj.trr

Here is my mdp file, should I remove entries for xtc_grps and
energygrps to avoid this issue?

integrator = md
nsteps = 5
dt = 0.002
nstvout = 5000
nstlog = 500
nstenergy = 250
nstxtcout = 5000
nstxout = 5000
xtc_grps = Protein LIG
energygrps = Protein  SOL
constraints = all-bonds
nstcomm = 1
ns_type = grid
rlist = 1.2
rcoulomb = 1.1
rvdw = 1.0
vdwtype = shift
rvdw-switch = 0.9
coulombtype = PME-Switch
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 300 300
Pcoupl = parrinello-rahman
PcOupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
lincs-iter = 2
DispCorr = EnerPres
optimize_fft = yes
gen_seed = 805087
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Re: [gmx-users] gromacs doubt

[Justin A. Lemkul]

manjula kasinathan wrote:


hi all

   i have done protein protein interaction and the complex structure
  was taken for MD simulation using Gromacs.while performing mdrun step 
for position restrain i got error. i have carried out mdrun for 1ps and 
the command given for mdrun

  and position restrain are
grompp -f *.pdb -c *.gro -p top.top -o *.tpr
mdrun -v -deffnm pr
my em.mdp file

title   = com
cpp = /usr/local/gromacs/share/gromacs/cpp ; the c 
pre-processor


Not that this matters (since cpp is ignored in Gromacs 4.0.x and would have 
caused a serious error in the 3.3.x series), but Gromacs does not distribute a 
cpp, so this line is nonsense.  Just FYI.



define  = -DFLEXIBLE
constraints = none
integrator  = steep
dt  = 0.002; ps !
nsteps  = 3000
nstlist = 10
ns_type = grid
rlist   = 1.0
coulombtype = PME
rcoulomb= 1.0
vdwtype = cut-off
rvdw= 1.4
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
;
;Energy minimizing stuff
;
emtol   = 1000.0
emstep  = 0.01.

here i have given nsteps 3000. but while doing energy minimization it 
considers only 1000 steps and the energy was minimized for only 1000 
steps. then i gone for position restrain step while doing Mdrun i got 
error like this




And what was the output from the energy minimization?  Are the resulting 
potential energy and maximum force acceptable?  Have you checked the output 
configuration from any unresolved clashes?


-Justin


starting mdrun 'Protein in water'
500 steps,  1.0 ps.
step 400, remaining runtime:   132 s 
Step 402, time 0.804 (ps)  LINCS WARNING

relative constraint deviation after LINCS:
rms 0.000119, max 0.006712 (between atoms 2873 and 2875)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2873   2875   64.40.0989   0.1007  0.1000

t = 0.868 ps: Water molecule starting at atom 93766 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

wat should i do now. how can i progress this.could any one help me plz. 
thank in advance


Cheers,
Manjula Kasinathan.



--


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


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Re: [gmx-users] xmgrace

[Oliver Grant]

Command is xmgrace and it needs to be in your $PATH.

On 13 May 2010 12:19, shahid nayeem  wrote:

> Dear all
> I downloaded xmgr-4.1.2.tar.gz and tried to install by following commands.
> tar -xvzf xmgr-4.1.2.tar.gz
> cd xmgr-4.1.2
> ./configure
> make
> make install
> But it gives error command xmgr not found.
> Please help.
> shahid Nayeem
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[gmx-users] xmgrace

[shahid nayeem]

Dear all
I downloaded xmgr-4.1.2.tar.gz and tried to install by following commands.
tar -xvzf xmgr-4.1.2.tar.gz
cd xmgr-4.1.2
./configure
make
make install
But it gives error command xmgr not found.
Please help.
shahid Nayeem
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Re: [gmx-users] RE: .rtp libraries

[Tsjerk Wassenaar]

Hi Stephen,

> I am particularly interested in lipid .rtp libraries hopefully for something 
> that has all-atom force fields, as I personally believe simulations should be 
> as real as possible, and also believe non-polar hydrogens still illicite some 
> force in the overall scheme of the molecular simulation.

Yes, of course they do. And don't forget charge transfer effects,
polarization and quantum effects. But you can't have it all. Every
model has its domain of application and its pros and cons.

> As most lipid systems in cells are insanly complec, many lipid types in many 
> proportions and chain lengths, etc... I woundered if somone(s) has already 
> constructed a library with the 200 or so outer membrane lipids.  I did read 
> years back about mitochondrial simulations, which did include dozens of 
> lipids, even cardiolipin, etc...but never found libraries.

References would be good. I know there's a good deal of effort on
parameterization of lipids, especially in the group of Tieleman, as
well as in ours. But an encompassing library of lipid models seems to
be a bit too much to ask for at the moment. Parameterization is a
tricky process, especially if the experimental data on pure lipids and
controlled mixtures is scarce. Any such library should be used with
caution, i.e. with background reading of the methods and assumptions
used for the parameterization.

> Happy Ascention

Errm, I wasn't intending on going yet... :p

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
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Re: [gmx-users] RE: .rtp libraries

[Esteban Gabriel Vega Hissi]

Hi Stephen,
Is it possible for you to post the link to the articles you read about
mitochondrial simulations and the 200 membrane lipids?

Thanks in advance

Esteban

On Thu, May 13, 2010 at 12:00 PM, lloyd riggs  wrote:

>
> Dear All,
>
> I recentlly started using Gromacs again.  I was just woundering if anyone
> had some .rtp libraries available to add on to the software, or for VMD.
>
> I am particularly interested in lipid .rtp libraries hopefully for
> something that has all-atom force fields, as I personally believe
> simulations should be as real as possible, and also believe non-polar
> hydrogens still illicite some force in the overall scheme of the molecular
> simulation.  As most lipid systems in cells are insanly complec, many lipid
> types in many proportions and chain lengths, etc... I woundered if somone(s)
> has already constructed a library with the 200 or so outer membrane lipids.
>  I did read years back about mitochondrial simulations, which did include
> dozens of lipids, even cardiolipin, etc...but never found libraries.
>
> In addition, and other add on libraries which may be trusted, or based on
> empirical data would be greattly appriciated.
>
> I personally was just going to add them into the .rtp libraries (of which
> they are compatible) if anyone has them available.
>
> Happy Ascention
>
> Stephen Watkins
> --
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>
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[gmx-users] RE: .rtp libraries

[lloyd riggs]

Dear All,

I recentlly started using Gromacs again.  I was just woundering if anyone had 
some .rtp libraries available to add on to the software, or for VMD.

I am particularly interested in lipid .rtp libraries hopefully for something 
that has all-atom force fields, as I personally believe simulations should be 
as real as possible, and also believe non-polar hydrogens still illicite some 
force in the overall scheme of the molecular simulation.  As most lipid systems 
in cells are insanly complec, many lipid types in many proportions and chain 
lengths, etc... I woundered if somone(s) has already constructed a library with 
the 200 or so outer membrane lipids.  I did read years back about mitochondrial 
simulations, which did include dozens of lipids, even cardiolipin, etc...but 
never found libraries.

In addition, and other add on libraries which may be trusted, or based on 
empirical data would be greattly appriciated.  

I personally was just going to add them into the .rtp libraries (of which they 
are compatible) if anyone has them available.

Happy Ascention

Stephen Watkins
-- 
GMX.ch - Schweizer FreeMail-Dienst mit über 800.000 Mitgliedern
E-Mail & mehr! Kostenlos: http://portal.gmx.net/de/go/chfreemail
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[gmx-users] gromacs doubt

[manjula kasinathan]

hi all

   i have done protein protein interaction and the complex structure
  was taken for MD simulation using Gromacs.while performing mdrun step for
position restrain i got error. i have carried out mdrun for 1ps and the
command given for mdrun
  and position restrain are
grompp -f *.pdb -c *.gro -p top.top -o *.tpr
mdrun -v -deffnm pr
my em.mdp file

title   = com
cpp = /usr/local/gromacs/share/gromacs/cpp ; the c
pre-processor
define  = -DFLEXIBLE
constraints = none
integrator  = steep
dt  = 0.002; ps !
nsteps  = 3000
nstlist = 10
ns_type = grid
rlist   = 1.0
coulombtype = PME
rcoulomb= 1.0
vdwtype = cut-off
rvdw= 1.4
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
;
;Energy minimizing stuff
;
emtol   = 1000.0
emstep  = 0.01.

here i have given nsteps 3000. but while doing energy minimization it
considers only 1000 steps and the energy was minimized for only 1000 steps.
then i gone for position restrain step while doing Mdrun i got error like
this

starting mdrun 'Protein in water'
500 steps,  1.0 ps.
step 400, remaining runtime:   132 s
Step 402, time 0.804 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000119, max 0.006712 (between atoms 2873 and 2875)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2873   2875   64.40.0989   0.1007  0.1000

t = 0.868 ps: Water molecule starting at atom 93766 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

wat should i do now. how can i progress this.could any one help me plz.
thank in advance

Cheers,
Manjula Kasinathan.
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