[gmx-users] Re: MOPAC gromacs mdreun error (vidhya sankar)

[Gerrit Groenhof]

> 
>   2. MOPAC gromacs mdreun error (vidhya sankar)

It seems that you are trying to run with multiple threads. Use mdrun -nt 1 to 
use only a single thread.

Gerrit


> Dear gmx users
> 
> i have successfuly installed Mopac gromacs/interface. but when i run 
> the QM/MM in mdrun_d 
>  i have got hte following error 
> QM/MM calculation requested.
> QM/MM calculation requested.
> there we go!
> there we go!
> Segmentation fault (core dumped)
> i am using 6 atoms for my Qm region i am using fedora core13 OS and pentium 
> intel i5
> what could i do to remove this error
> ?
> i am expecting your reply soon  thanks in advance
> 
> 
> 
--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/

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[gmx-users] Change in structure after solvation_Gromacs

[swagata chakraborty]

Hi,

I was trying to run MD simulation of my protein in DMSO. I used the force
field ffG53a6 and did the energy minimization after solvating the protein in
DMSO box.
But after solvating in DMSO, the structure is changing. My protein is a
homodimer and the loop at the dimer interface is converting into a sheet.
Please suggest where I am going wrong since the structure shouldnot change
after solvation.


Regards
Swagata Chakraborty
Research Scholar,
Department of Chemical Sciences,
Tata Institute of Fundamental Research,
Mumbai-45
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Re: [gmx-users] Change in structure after solvation_Gromacs

[ms]

On 05/12/10 10:39, swagata chakraborty wrote:

I was trying to run MD simulation of my protein in DMSO. I used the force
field ffG53a6 and did the energy minimization after solvating the protein in
DMSO box.
But after solvating in DMSO, the structure is changing. My protein is a
homodimer and the loop at the dimer interface is converting into a sheet.
Please suggest where I am going wrong since the structure shouldnot change
after solvation.


You're not giving nearly enough detail (what is the dmso/water ratio? 
what is your .mdp file?) etc.


In any case, it wouldn't be the first time that simulations and 
experiments disagree. How do you *know* that structure shouldn't change? 
Have you tried using another force field, like OPLS?


--
Massimo Sandal, Ph.D.
http://devicerandom.org
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[gmx-users] LINCS WARNING

[Raymond.nuist]

Dear users
  Here is my problem:
  I just changed my GMX version from 4.0 to 4.5.
  But the task was in a Segmentation fault, whileI can "mdrun" it well in 
4.0 environment .
 

  Here is the error:




Step 1902, time 1.902 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1057.527961, max 39594.472656 (between atoms 5543 and 5541)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 1902, time 1.902 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 598.238330, max 39421.507812 (between atoms 5544 and 5546)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2136   2138   32.40.1759   0.1096  0.1096
   6874   6869   44.60.1103   0.1082  0.1082
   5728   5727   90.00.   0.2223  0.1090
   7024   7023   90.00.   0.1591  0.1090
   7025   7023   90.00.   2.7347  0.1090
   7027   7026   90.00.1118   2.7603  0.1096
   7028   7026   90.00.1118   1.7013  0.1096
   7029   7030   90.00.1559   0.2336  0.1096
   7029   7031   90.00.2080   2.4955  0.1096
   8377   8376   41.30.1118   0.1095  0.1096
   8385   8382  143.80.1115   2.5694  0.1094
   8384   8382   90.00.1115   0.2055  0.1094
   5684   5682   42.60.1118   0.1096  0.1096
   8383   8382   90.00.1115   0.2720  0.1094
   5436   5435   34.80.1113   2.4639  0.1092
   5437   5435   90.00.1113   0.8917  0.1092
   5438   5435   90.00.1113   0.2059  0.1092
   5530   5525   95.50.1637  46.5184  0.1082
   5536   5535   90.00.  63.8121  0.1090
   5537   5535  110.70.   2.1859  0.1090
   5539   5538   90.00.1118   5.2483  0.1096
   5540   5538   90.00.1118   0.5557  0.1096
   5542   5541  105.90.1118   4.8490  0.1096
   5543   5541   90.00.1118 4340.0601  0.1096
   5480   5473   54.70.1103   0.1082  0.1082
   5545   5544   89.40.1118  18.5327  0.1096
   5544   5546   90.00.2399 4321.1011  0.1096
   5245   5243   36.60.1113   0.1093  0.1092
   2794   2789   90.00.1103   0.3056  0.1082
   4160   4158   90.00.1115   0.1108  0.1094
   8456   8449   90.00.1103   3.7825  0.1082
   7029   7030   90.00.1559   0.2336  0.1096
   4520   4513   90.00.1103   0.2065  0.1082
   7029   7031   90.00.2080   2.4955  0.1096
   7033   7032   90.00.1118   2.6289  0.1096
   7034   7032   90.00.1118   0.4015  0.1096
   4524   4523   65.10.1113   0.1091  0.1092
  10281  10276   68.70.1105   0.1083  0.1083
   7041   7038   35.70.1115   0.1094  0.1094
   2136   2138   32.40.1759   0.1096  0.1096
  10282  10277   90.00.1103   0.1607  0.1082
  10288  10287   90.00.   0.3496  0.1090
   5544   5546   90.00.2399 4321.1011  0.1096
   5544   5545   89.40.1118  18.5327  0.1096
   5548   5547   90.00.1118   1.0539  0.1096
   5549   5547   48.50.1118   0.1038  0.1096
   2800   2799   90.00.   2.8513  0.1090
   2801   2799   90.00.   0.6884  0.1090
  10291  10290   90.00.1118   0.1451  0.1096
   3520   3519   90.00.   1.1565  0.1090
   3521   3519   90.00.   0.7086  0.1090
   3525   3526   90.00.2190  12.9248  0.1096
   3525   3527   90.00.1127   0.1825  0.1096
   5494   5493   50.90.1118   0.1038  0.1096
   5495   5493   90.00.1118   1.3247  0.1096
   8460   8459   90.00.1113   1.3661  0.1092
   8461   8459   90.00.1113   0.2465  0.1092
   8462   8459   90.00.1113   0.2054  0.1092
   3525   3526   90.00.2190  12.9248  0.1096
   3525   3527   90.00.1127   0.1825  0.1096
   4528   4527   90.00.   1.1331  0.1090
   4529   4527   32.80.   0.1132  0.1090
   4531   4530   90.00.1118   0.1824  0.1096
   4532   4530   40.40.1118   3.0513  0.1096
   4535   4533   90.00.1118   0.1212  0.1096
  10280  10273   90.00.1103   0.3980  0.1082
   6648   6649   90.00.1118   2.0258  0.1096
   6653   6651   90.00.1118   1.9735  0.1096
   6657   6654   90.00.1115   2.2662  0.1094
   4522   4517   46.80.1103   0.1082  0.1082
   6646   6645   90.00.1117   1.3712  0.1096
   6985   6984   41.00.1118   0.1096  0.1096
   3529   3528   90.00.1118   0.1886  0.1096
   3530   3528   90.00.1118   0.1834  0.1096
   2991   2992   90.00.2281  61.6154  0.1090
   2991   2993   90.00.1982   0.3326  0.1090
   6647   6645   90.00.1118   0.6161  0.1096
   6649   6648   90.00.1118   2.0258  0.1096
   2997   2998   93.30.1771   9.1908  0.1096
   2997   2999   90.00.1311 517.9474  0.1096
   3574   3573   90.00.11

Re: [gmx-users] Restraining water

[Oliver Grant]

I would use grep and cut to take the atom numbers of the residues I want to
restrain and direct them into an index file with [res_sol] at the top. Then
use genrestr to generate restraints for these atoms using the -n option.
Then conditionally include this restraint file (.itp file) in my topology
when you use -DPOSRES_res_sol (or whatever just make it match what's in the
top file) in your mdp file.

Thats how I would put position restraints on parts of my system. I think
different constraints are answered here too :)
Good luck,
Oliver



On 2 December 2010 08:21, David Rodríguez wrote:

> 2010/12/2 Mark Abraham 
>
> On 2/12/2010 12:51 PM, Guido Polles wrote:
>>
>>> Hi,
>>> I know it looks a little bit strange, but i was trying to restrain
>>> just some water in my system.
>>> Now, if i put something like
>>> [ position_restraints ]
>>> ;  i funct   fcxfcyfcz
>>>11   1000   1000   1000
>>> I put restraints on all the molecules.
>>>
>>
>> Yes, that directive will pertain to all the molecules that have that [
>> moleculetype ]. I'm not sure if you only want position restraints on some of
>> your water molecules.
>>
>>
>>  I thought about a turnaround,  just making a second water molecule
>>> type, but now complains about using more than one settle type.
>>> Is there any other way to do it?
>>>
>>
> Guido,
> You may find this thread useful:
> http://lists.gromacs.org/pipermail/gmx-users/2010-September/054087.html
>
>
>> And if I follow the "Suggestion: change the least use settle
>>> constraints into 3 normal constraints" I have to worry about some kind
>>> of huge loss in performance?
>>>
>>
>> I would expect the non-settle waters to use the solvent-optimized loops in
>> the normal way, so there should be no difference in execution time between
>> the unrestrained all-settle simulation and the partly-restrained
>> party-settled simulation. Obviously, this is straightforward to test.
>>
>> Mark
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>
>
>
> --
> David Rodríguez Díaz, PhD Student
> Fundación Pública Galega de Medicina Xenómica (SERGAS)
> Web page: http://webspersoais.usc.es/persoais/david.rodriguez.diaz
>
> --
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Re: [gmx-users] dna, lipid simulation

[Itamar Kass (Med)]

Hi Amit,

The GROMOS force field had both DNA and lipids parameters, hence you can use
it in your simulations. Moreover, there are new lipids parameters by David
Poger and Alan Mark which I should give better results compared to the old
set.

Good luck.


On 5 December 2010 18:09, Amit Choubey  wrote:

> Hi all,
>
> This is a question unrelated to gromacs but would pose it anyway to get
> some hints from the experts.
> I wish to set up DNA and DPPC lipid membrane simulation. Could someone
> please refer to a relevant forcefield/tutorial for simulation of lipids with
> DNA?
>
> Any help will be really appreciated.
>
> Thank you
> amit
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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>



-- 

-- 


"In theory, there is no difference between theory and practice. But, in
practice, there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu

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Re: [gmx-users] dna, lipid simulation

[Justin A. Lemkul]

Amit Choubey wrote:

Hi all,

This is a question unrelated to gromacs but would pose it anyway to get 
some hints from the experts.
I wish to set up DNA and DPPC lipid membrane simulation. Could someone 
please refer to a relevant forcefield/tutorial for simulation of lipids 
with DNA?




I would suspect that the CHARMM force fields could cover this quite nicely.

There is no tutorial for exactly what you want, but in principal, is very 
similar to the membrane protein tutorial I wrote (see 
http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations), although 
if you choose to use CHARMM, there is no need to mess with topologies; 
everything you need should be built in.  The same fundamentals apply, though.


-Justin


Any help will be really appreciated.

Thank you
amit



--


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] Change in structure after solvation_Gromacs

[Justin A. Lemkul]

ms wrote:

On 05/12/10 10:39, swagata chakraborty wrote:

I was trying to run MD simulation of my protein in DMSO. I used the force
field ffG53a6 and did the energy minimization after solvating the 
protein in

DMSO box.
But after solvating in DMSO, the structure is changing. My protein is a
homodimer and the loop at the dimer interface is converting into a sheet.
Please suggest where I am going wrong since the structure shouldnot 
change

after solvation.


You're not giving nearly enough detail (what is the dmso/water ratio? 
what is your .mdp file?) etc.


In any case, it wouldn't be the first time that simulations and 
experiments disagree. How do you *know* that structure shouldn't change? 
Have you tried using another force field, like OPLS?




This might just be a visualization artifact, something that gets posted here 
routinely.  Some slight structural changes may have occurred during EM, such 
that the visualization program guess sheet instead of loop.  53A6 does tend to 
favor extended structures, but I would only suggest something is wrong if (1) a 
real simulation is conducted and the spurious secondary structure persists and 
(2) real analysis is done (like DSSP or STRIDE) to conclude the secondary 
structure, rather than just looking at it, as all visualization software uses 
different heuristics to assign structures.  It does not make for convincing 
evidence.


-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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Re: [gmx-users] LINCS WARNING

[Justin A. Lemkul]

Raymond.nuist wrote:

Dear users
  Here is my problem:
  I just changed my GMX version from 4.0 to 4.5.
  But the task was in a Segmentation fault, whileI can "mdrun" it 
well in 4.0 environment .
 


Providing an .mdp file and a description of your system would be useful.



  Here is the error:



This suggests nothing beyond physical instability of your system, i.e.:

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

-Justin





Step 1902, time 1.902 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1057.527961, max 39594.472656 (between atoms 5543 and 5541)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 1902, time 1.902 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 598.238330, max 39421.507812 (between atoms 5544 and 5546)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   2136   2138   32.40.1759   0.1096  0.1096
   6874   6869   44.60.1103   0.1082  0.1082
   5728   5727   90.00.   0.2223  0.1090
   7024   7023   90.00.   0.1591  0.1090
   7025   7023   90.00.   2.7347  0.1090
   7027   7026   90.00.1118   2.7603  0.1096
   7028   7026   90.00.1118   1.7013  0.1096
   7029   7030   90.00.1559   0.2336  0.1096
   7029   7031   90.00.2080   2.4955  0.1096
   8377   8376   41.30.1118   0.1095  0.1096
   8385   8382  143.80.1115   2.5694  0.1094
   8384   8382   90.00.1115   0.2055  0.1094
   5684   5682   42.60.1118   0.1096  0.1096
   8383   8382   90.00.1115   0.2720  0.1094
   5436   5435   34.80.1113   2.4639  0.1092
   5437   5435   90.00.1113   0.8917  0.1092
   5438   5435   90.00.1113   0.2059  0.1092
   5530   5525   95.50.1637  46.5184  0.1082
   5536   5535   90.00.  63.8121  0.1090
   5537   5535  110.70.   2.1859  0.1090
   5539   5538   90.00.1118   5.2483  0.1096
   5540   5538   90.00.1118   0.5557  0.1096
   5542   5541  105.90.1118   4.8490  0.1096
   5543   5541   90.00.1118 4340.0601  0.1096
   5480   5473   54.70.1103   0.1082  0.1082
   5545   5544   89.40.1118  18.5327  0.1096
   5544   5546   90.00.2399 4321.1011  0.1096
   5245   5243   36.60.1113   0.1093  0.1092
   2794   2789   90.00.1103   0.3056  0.1082
   4160   4158   90.00.1115   0.1108  0.1094
   8456   8449   90.00.1103   3.7825  0.1082
   7029   7030   90.00.1559   0.2336  0.1096
   4520   4513   90.00.1103   0.2065  0.1082
   7029   7031   90.00.2080   2.4955  0.1096
   7033   7032   90.00.1118   2.6289  0.1096
   7034   7032   90.00.1118   0.4015  0.1096
   4524   4523   65.10.1113   0.1091  0.1092
  10281  10276   68.70.1105   0.1083  0.1083
   7041   7038   35.70.1115   0.1094  0.1094
   2136   2138   32.40.1759   0.1096  0.1096
  10282  10277   90.00.1103   0.1607  0.1082
  10288  10287   90.00.   0.3496  0.1090
   5544   5546   90.00.2399 4321.1011  0.1096
   5544   5545   89.40.1118  18.5327  0.1096
   5548   5547   90.00.1118   1.0539  0.1096
   5549   5547   48.50.1118   0.1038  0.1096
   2800   2799   90.00.   2.8513  0.1090
   2801   2799   90.00.   0.6884  0.1090
  10291  10290   90.00.1118   0.1451  0.1096
   3520   3519   90.00.   1.1565  0.1090
   3521   3519   90.00.   0.7086  0.1090
   3525   3526   90.00.2190  12.9248  0.1096
   3525   3527   90.00.1127   0.1825  0.1096
   5494   5493   50.90.1118   0.1038  0.1096
   5495   5493   90.00.1118   1.3247  0.1096
   8460   8459   90.00.1113   1.3661  0.1092
   8461   8459   90.00.1113   0.2465  0.1092
   8462   8459   90.00.1113   0.2054  0.1092
   3525   3526   90.00.2190  12.9248  0.1096
   3525   3527   90.00.1127   0.1825  0.1096
   4528   4527   90.00.   1.1331  0.1090
   4529   4527   32.80.   0.1132  0.1090
   4531   4530   90.00.1118   0.1824  0.1096
   4532   4530   40.40.1118   3.0513  0.1096
   4535   4533   90.00.1118   0.1212  0.1096
  10280  10273   90.00.1103   0.3980  0.1082
   6648   6649   90.00.1118   2.0258  0.1096
   6653   6651   90.00.1118   1.9735  0.1096
   6657   6654   90.00.1115   2.2662  0.1094
   4522   4517   46.80.1103   0.1082  0.1082
   6646   6645   90.00.1117   1.3712  0.1096
   6985   6984   41.00.1118   0.1096  0.1096
   3529   3528   90.00.1118   0.1886  0.1096
   3530   3528   90.00.1118   0.1834  0.1096
   2991   2992   90.00.2281  61.6154  0.1090
   2991   2993   90.00.1982   0.3326  

Re: [gmx-users] Change in structure after solvation_Gromacs

[ms]

On 05/12/10 13:20, Justin A. Lemkul wrote:



ms wrote:

On 05/12/10 10:39, swagata chakraborty wrote:

I was trying to run MD simulation of my protein in DMSO. I used the
force
field ffG53a6 and did the energy minimization after solvating the
protein in
DMSO box.
But after solvating in DMSO, the structure is changing. My protein is a
homodimer and the loop at the dimer interface is converting into a
sheet.
Please suggest where I am going wrong since the structure shouldnot
change
after solvation.


You're not giving nearly enough detail (what is the dmso/water ratio?
what is your .mdp file?) etc.

In any case, it wouldn't be the first time that simulations and
experiments disagree. How do you *know* that structure shouldn't
change? Have you tried using another force field, like OPLS?



This might just be a visualization artifact, something that gets posted
here routinely. Some slight structural changes may have occurred during
EM, such that the visualization program guess sheet instead of loop.
53A6 does tend to favor extended structures, but I would only suggest
something is wrong if (1) a real simulation is conducted and the
spurious secondary structure persists and (2) real analysis is done
(like DSSP or STRIDE) to conclude the secondary structure, rather than
just looking at it, as all visualization software uses different
heuristics to assign structures. It does not make for convincing evidence.



You are absolutely right (as almost always you are!), yet more detail, 
the better. I'd say that visualizing it in Pymol using the dss command 
to give the DSSP assignment could help.


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[gmx-users] Re: Re: Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?

[sa]

Dear all,

I come back to you with my problem between -chargegrp and -nochargegrp with
new results which are contradict my previous
findings. Indeed, in my previous message i have suggested that the
discrepancies between -chargegrp and -nochargegrp in
my simulations of a 25 AA peptide in TIP3P water. I suspect that this
discrepancy came probably from an old version of the CHARMM27 ff and the
used in my simulations. To test this hypothesis i have done six additional
simulations of the same system (a 25 AA peptide in TIP3P water) with the new
released of the CHARMM27 ff and gromacs versions 4.5.1 and 4.5.3

I have done three simulation of with a *.top file generated by pdb2gromacs
v. 4.5.3 and modified by hand to change the charge
groups distribution in the peptide atoms according to the original CHARMM
force field and to mimic the -chargegrp option
available in the previous version of gromacs.
Three others MD were also done with *.top generated with pdb2gromacs of
gromacs 4.5.3 (i.e. with one charge group per atom).

1- gromacs4.5.1 and CHARMM27.ff -> gromacs 4.5.1*
2- gromacs4.5.3 and CHARMM27.ff -> gromacs 4.5.3*
3- gromacs4.5.3 and CHARMM27.ff and MD parameters used by Bjelkmar et al.
(J. Chem. Theory Comput. 2010, 6,
459–466-> gromacs 4.5.3**

non-bonded md parameters used in * simulations

>> continuation= no; Restarting after NPT
>> vdw-type= cut-off
>> rvdw= 1.0
>> rlist   = 0.9
>> coulombtype  = PME
>> rcoulomb = 0.9
>> fourierspacing   = 0.12
>> fourier_nx   = 0
>> fourier_ny   = 0
>> fourier_nz   = 0
>> pme_order= 4
>> ewald_rtol   = 1e-05
>> optimize_fft= yes

To summarize, as shown in the two figures accessible with the two links
below (hosted by hostingpics.net), all the peptides remain in their helix
conformation and no significant differences were observed with the md
parameters, the gromacs version and finally how  the charge group
distribution to compute the force during the simulations.

http://hpics.li/9ed5ee1  --> Secondary structure vs. time

http://hpics.li/7cf1625  --> RMSD vs. time

So i suspect that the errors come from the use a bad version of the CHARMM27
ff

Thank you all for your preceding comments

SA

Francesco Oteri wrote:
> > To see if the problem is force-field related, you could try to run the
> > same simulations using amber-ff.
> > If you will find the same results, probably is a software bug.
> >
>
> Some Amber parameter sets (Amber94, I think) have issues of being overly
> "helix-friendly," but perhaps other force fields, in general, might make
> for
> good comparisons.  But then, too, Gromos96 over-stabilizes extended
> conformations, so buyer beware...
>
> > Maybe the bug has been introduced in the version 4 when the Domain
> > Decomposition has been introduced.
> > You can check if it is a software problem using the 3.3.3 version.
> >
>
> I doubt that would work.  There have been many code changes in order to
> implement CHARMM.  If anything, try mdrun -pd to use the old particle
> decomposition mode, but I would be very hesitant to blindly say that DD
> might be
> causing this behavior.
>
> -Justin
>
> >
> >
> >
> > Il 25/11/2010 23:42, sa ha scritto:
> >> Dear All,
> >>
> >> In a previous message
> >> (http://lists.gromacs.org/pipermail/gmx-users/2010-November/055839.html
> ),
> >> I described the results obtained with MD performed with the CHARMM27
> >> ff and the chargegrp "yes" and "no" options of a peptide in TIP3P
> >> water simulated gromacs. Since these results puzzled me a lot, i would
> >> like to share with you others results obtained from the gromacs
> >> community advices to explain these results.
> >>
> >> In few words, the context of these simulations. One of my labmate did,
> >> 8 months ago (march/april), several simulations of a peptide (25 AA)
> >> with the CHARMM27 ff (and CMAP). The peptide is a transmembrane
> >> segment (TM) and belongs to a large membrane protein. This TM segment
> >> has an initial helical conformation. The simulations were performed in
> >> a cubic box filled with app. 14000 TIP3P water (Jorgensen's model)
> >> with 2 Cl ions. To construct the topology file of the system,
> >> -chargegrp "yes" with pdb2gmx and the MD were done with the gromacs
> >> 4.0.5. For some reasons, he had to left the lab, and my boss asked me
> >> to continue his work. When I checked their results, i was very
> >> intrigued by these MD results because he found that the peptide keep
> >> along all the simulation time (100 ns) its initial helical
> >> conformation. This results are not in agreement with circular
> >> dichroism experiments which are shown that the same peptide in water
> >> has no helix segment and is completely unfold. I am aware that the
> >> simulation time is short compared to experiment time scale, however
> >> since i haven't seen any unfolding events in this simulati

Re: [gmx-users] g_hbond results inconsistent between v4.0.7 and v4.5.1

[Robin C. Underwood]

Hi All:

Has there been further resolution on the difference between g_hbond in v 4.0 and
4.5 (I'm running 4.5.3)? For counting water-water (tip4p) h-bonds in a box of
506 waters I get the following nhbdist output, which appears to neglect pbc
since there are such a large number of unbound donor-H (and the other columns
are consequently too low):


@title "Number of donor-H with N HBs"
@xaxis  label "Time (ps)"
@yaxis  label "N"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 HBs"
@ s1 legend "1 HB"
@ s2 legend "2 HBs"
@ s3 legend "3 HBs"
@ s4 legend "Total"
 0.0e+00   706   174   132 0   438
 1.0e-01   708   163   140 1   446
 2.0e-01   707   168   137 0   442
 3.0e-01   712   161   136 3   442
 4.0e-01   713   165   134 0   433
 5.0e-01   709   169   133 1   438
 6.0e-01   705   169   137 1   446
 7.0e-01   699   169   142 2   459
 8.0e-01   710   167   133 2   439
 9.0e-01   700   189   122 1   436
 1.0e+00   707   169   136 0   441
 1.1e+00   705   163   144 0   451
 1.2e+00   707   171   133 1   440
 1.3e+00   709   158   145 0   448
 1.4e+00   718   155   138 1   434
 1.5e+00   711   164   137 0   438
 1.6e+00   713   160   139 0   438
 1.7e+00   702   181   129 0   439
 1.8e+00   707   162   142 1   449
 1.9e+00   706   167   139 0   445
 2.0e+00   709   168   135 0   438
 2.1e+00   708   167   136 1   442
 2.2e+00   708   171   133 0   437
 2.3e+00   709   162   140 1   445
 2.4e+00   698   171   142 1   458
 2.5e+00   701   177   133 1   446
 2.6e+00   706   177   129 0   435
 2.7e+00   708   178   126 0   430
 2.8e+00   698   187   127 0   441
 2.9e+00   700   190   120 2   436
 3.0e+00   703   176   131 2   444
 3.1e+00   702   181   127 2   441
 3.2e+00   694   184   134 0   452


I've tried playing with different index assignments, and I get what appears to
be a reasonable output for "0 HBs" by making the two groups appear different,
excluding the dummy atom from one. Although, because the program then double
counts, the other columns don't convey the intended information. 


Robin 






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Chemistry Department
560 Oval Drive
West Lafayette, IN 47907
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[gmx-users] Re: polymer simulations in gromacs

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private help service.


I do not do polymer simulations, nor do I have any real clue as to how to help 
you, aside from suggesting the following, which may or may not be relevant:


http://www.gromacs.org/Documentation/How-tos/Polymers
http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

I am CC'ing this message to the list.  Please keep all further posts there, as 
perhaps someone can actually help you.


-Justin

Björn Nadrowski wrote:
Hi Justin, 
I just found out that you are simulating polymers using gromacs. 
I would like to do the same stuff, but from a much less molecular angle.
I am the only one here that does that stuff, so I have to jump through all the loops myself, 
and the gromacs loop is really tiny and hard to jump through. 

Ideally, I would just like to define my polymer as a succession of identical nodes, 
that have a user(i.e. defined by me) interaction potential (essentially hard core repulsion with an 
intermedeiate attractive regime), some 3-node angle stiffness term, friction (no water! Just the polymers with friction!), 
position restraints (all bonds between the nodes should be constrained to have the same length), and
some boundary conditions. 


How would I go about that?
I have scanned the documentation, but I am beaten to death by its volume, where 
most of it concerns stuff I am not
interested in. Ideally, I would like to represent my nodes as some kind of idealistic atom with said interactions. 
However, I do not find the part where I define such an atom, or how to do that. 
Can you point me to some source where I might get a nice simple tutorial of how to define such an elementary node, and its interactions?


Thanks, Bjoern




--


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] Re: polymer simulations in gromacs

[ms]

On 05/12/10 19:41, Justin A. Lemkul wrote:


Please keep all Gromacs-related correspondence on the gmx-users list. I
am not a private help service.

I do not do polymer simulations, nor do I have any real clue as to how
to help you, aside from suggesting the following, which may or may not
be relevant:

http://www.gromacs.org/Documentation/How-tos/Polymers
http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

I am CC'ing this message to the list. Please keep all further posts
there, as perhaps someone can actually help you.

-Justin

Björn Nadrowski wrote:

Hi Justin, I just found out that you are simulating polymers using
gromacs. I would like to do the same stuff, but from a much less
molecular angle.
I am the only one here that does that stuff, so I have to jump through
all the loops myself, and the gromacs loop is really tiny and hard to
jump through.
Ideally, I would just like to define my polymer as a succession of
identical nodes, that have a user(i.e. defined by me) interaction
potential (essentially hard core repulsion with an intermedeiate
attractive regime), some 3-node angle stiffness term, friction (no
water! Just the polymers with friction!), position restraints (all
bonds between the nodes should be constrained to have the same
length), and
some boundary conditions.
How would I go about that?
I have scanned the documentation, but I am beaten to death by its
volume, where most of it concerns stuff I am not
interested in. Ideally, I would like to represent my nodes as some
kind of idealistic atom with said interactions. However, I do not find
the part where I define such an atom, or how to do that. Can you point
me to some source where I might get a nice simple tutorial of how to
define such an elementary node, and its interactions?



Hi Bjoern,
Your experience is much like mine -I am actually doing something very 
similar, a coarse grain to model proteins which has very very similar 
features (I even suspect we're starting from the same literature, given 
the description). My advice is:


- Read the documentation. Multiple times. Understand it. *All* of it 
concerns stuff you *will* be interested in (apart perhaps some specific 
analysis tool, but even there...). Yes, it's long, but there's no hope 
of going anywhere without knowing it.
- Look at how residues and force fields are defined. Learn to create 
your own force field. The easiest thing is probably taking an existent 
force field, duplicate it and then work on the copy customizing it to 
your liking (That's what I did).
- Also, look at how protein residues are defined for use with pdb2gmx 
etc. - even if you are designing a non-protein polymer, it all basically 
starts from there, you then edit the residues etc. until you get the 
"unit" you want.
- Learn about tables and tabulated potentials if VdW functions are not 
enough.

- Learn about charge groups, energy groups etc.
- Remember that hardcore repulsion doesn't play well with MD 
integration: you'll spend a lot of time tuning it to be stiff enough but 
not too much to make your system explode

- About friction, do you mean Langevin dynamics?
- Do a lot of tests :)

It's very general advice, I know, but there's no real tutorial for such 
a thing, every custom model is... custom, and everyone, wanting 
different things, is quite on its own.


Best of luck! It took me about 1 - 1.2 years to get the model begin to 
work, so be patient and don't despair!


cheers,
M.

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Re: [gmx-users] dna, lipid simulation

[Thomas Piggot]

I would tend to agree with Justin rather than Itamar. The GROMOS DNA 
parameters are not especially good (see 
http://www.ncbi.nlm.nih.gov/pubmed/20614923) but it depends on what you 
are wanting to look at. Another option (rather than CHARMM, which for 
what it is worth is the force field I would probably use) is you could 
use one of the AMBER forcefields for the DNA and the GAFF lipids 
(although I forget if there is DPPC available or not, I think the only 
fully saturated lipid already available might be DMPC), but keep in mind 
you need to use surface tension with these lipids. As I said the choice 
really depends on what you want to look at, so some reading of the 
literature and also seeing what other people have done for similar 
simulations should help.


Cheers

Tom

On 05/12/10 12:42, Itamar Kass (Med) wrote:

Hi Amit,

The GROMOS force field had both DNA and lipids parameters, hence you 
can use it in your simulations. Moreover, there are new lipids 
parameters by David Poger and Alan Mark which I should give better 
results compared to the old set.


Good luck.


On 5 December 2010 18:09, Amit Choubey > wrote:


Hi all,

This is a question unrelated to gromacs but would pose it anyway
to get some hints from the experts.
I wish to set up DNA and DPPC lipid membrane simulation. Could
someone please refer to a relevant forcefield/tutorial for
simulation of lipids with DNA?

Any help will be really appreciated.

Thank you
amit

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--

--


"In theory, there is no difference between theory and practice. But, 
in practice, there is." - Jan L.A. van de Snepscheut


===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu 



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University of Southampton, UK.

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Re: [gmx-users] g_hbond results inconsistent between v4.0.7 and v4.5.1

[Erik Marklund]

Hi,

No. But I hope to get it done this week. Thanks for the reminder.

Erik

Robin C. Underwood skrev 2010-12-05 19.19:

Hi All:

Has there been further resolution on the difference between g_hbond in v 4.0 and
4.5 (I'm running 4.5.3)? For counting water-water (tip4p) h-bonds in a box of
506 waters I get the following nhbdist output, which appears to neglect pbc
since there are such a large number of unbound donor-H (and the other columns
are consequently too low):


@title "Number of donor-H with N HBs"
@xaxis  label "Time (ps)"
@yaxis  label "N"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 HBs"
@ s1 legend "1 HB"
@ s2 legend "2 HBs"
@ s3 legend "3 HBs"
@ s4 legend "Total"
  0.0e+00   706   174   132 0   438
  1.0e-01   708   163   140 1   446
  2.0e-01   707   168   137 0   442
  3.0e-01   712   161   136 3   442
  4.0e-01   713   165   134 0   433
  5.0e-01   709   169   133 1   438
  6.0e-01   705   169   137 1   446
  7.0e-01   699   169   142 2   459
  8.0e-01   710   167   133 2   439
  9.0e-01   700   189   122 1   436
  1.0e+00   707   169   136 0   441
  1.1e+00   705   163   144 0   451
  1.2e+00   707   171   133 1   440
  1.3e+00   709   158   145 0   448
  1.4e+00   718   155   138 1   434
  1.5e+00   711   164   137 0   438
  1.6e+00   713   160   139 0   438
  1.7e+00   702   181   129 0   439
  1.8e+00   707   162   142 1   449
  1.9e+00   706   167   139 0   445
  2.0e+00   709   168   135 0   438
  2.1e+00   708   167   136 1   442
  2.2e+00   708   171   133 0   437
  2.3e+00   709   162   140 1   445
  2.4e+00   698   171   142 1   458
  2.5e+00   701   177   133 1   446
  2.6e+00   706   177   129 0   435
  2.7e+00   708   178   126 0   430
  2.8e+00   698   187   127 0   441
  2.9e+00   700   190   120 2   436
  3.0e+00   703   176   131 2   444
  3.1e+00   702   181   127 2   441
  3.2e+00   694   184   134 0   452


I've tried playing with different index assignments, and I get what appears to
be a reasonable output for "0 HBs" by making the two groups appear different,
excluding the dummy atom from one. Although, because the program then double
counts, the other columns don't convey the intended information.


Robin









--
---
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
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er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] dna, lipid simulation

[Amit Choubey]

Thank you all. At least now I have an idea of the starting point.

On Sun, Dec 5, 2010 at 12:31 PM, Thomas Piggot  wrote:

>  I would tend to agree with Justin rather than Itamar. The GROMOS DNA
> parameters are not especially good (see
> http://www.ncbi.nlm.nih.gov/pubmed/20614923) but it depends on what you
> are wanting to look at. Another option (rather than CHARMM, which for what
> it is worth is the force field I would probably use) is you could use one of
> the AMBER forcefields for the DNA and the GAFF lipids (although I forget if
> there is DPPC available or not, I think the only fully saturated lipid
> already available might be DMPC), but keep in mind you need to use surface
> tension with these lipids. As I said the choice really depends on what you
> want to look at, so some reading of the literature and also seeing what
> other people have done for similar simulations should help.
>
> Cheers
>
> Tom
>
>
> On 05/12/10 12:42, Itamar Kass (Med) wrote:
>
> Hi Amit,
>
> The GROMOS force field had both DNA and lipids parameters, hence you can
> use it in your simulations. Moreover, there are new lipids parameters by
> David Poger and Alan Mark which I should give better results compared to the
> old set.
>
> Good luck.
>
>
> On 5 December 2010 18:09, Amit Choubey  wrote:
>
>> Hi all,
>>
>>  This is a question unrelated to gromacs but would pose it anyway to get
>> some hints from the experts.
>> I wish to set up DNA and DPPC lipid membrane simulation. Could someone
>> please refer to a relevant forcefield/tutorial for simulation of lipids with
>> DNA?
>>
>>  Any help will be really appreciated.
>>
>>  Thank you
>> amit
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
>
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> "In theory, there is no difference between theory and practice. But, in
> practice, there is." - Jan L.A. van de Snepscheut
>
> ===
> | Itamar Kass, Ph.D.
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> |
> | Department of Biochemistry and Molecular Biology
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> | Victoria 3800
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[gmx-users] : MOPAC gromacs mdreun error (vidhya sankar)

[vidhya sankar]

Dear Gerrit  sir,
   Thank you for your previous reply i tried as u said with  -nt 1 
option in mdrun but still i have got hte following error when i run mdrun_d
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 2
QMlevel: PM3/STO-3G
Program mdrun_d, VERSION 4.5.3
Source code file: qmmm.c, line: 697
Fatal error:
Semi-empirical QM only supported with Mopac.
 but i configured gromacs properly with mopac. how to solve the problem 
 is ther is any link that i have not made available ? i am expecting your 
worthfull reply thanks isn advance





--- On Sun, 5/12/10, Gerrit Groenhof  wrote:

From: Gerrit Groenhof 
Subject: [gmx-users] Re: MOPAC gromacs mdreun error (vidhya sankar)
To: gmx-users@gromacs.org
Date: Sunday, 5 December, 2010, 3:22 PM

> 
>   2. MOPAC gromacs mdreun error (vidhya sankar)

It seems that you are trying to run with multiple threads. Use mdrun -nt 1 to 
use only a single thread.

Gerrit


> Dear gmx users
>                     
> i have successfuly installed Mopac gromacs/interface. but when i run 
> the QM/MM in mdrun_d 
>  i have got hte following error 
> QM/MM calculation requested.
> QM/MM calculation requested.
> there we go!
> there we go!
> Segmentation fault (core dumped)
> i am using 6 atoms for my Qm region i am using fedora core13 OS and pentium 
> intel i5
> what could i do to remove this error
> ?
> i am expecting your reply soon  thanks in advance
> 
> 
> 
--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/

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[gmx-users] Crashed run

[shiva birgani]

Dear Justin
I had a crashed run and continued it by tpbconv and mdrun. After that in
order to analysis the results of new MD run I used of this command
trjcat -s md2.tpr -settime
But when I want to compute RMSD, DSSP, ... I do not know how I can put
together the results of MD1 (crashed run) and MD2 (continued one) to have
the homogeneous results.
Could you please help me in this regard?
thanks in advance
Shiva
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RE: [gmx-users] Crashed run

[Shi Wenxiong (Dr)]

I think you can use the command "trjcat -f MD1.xtc MD2.xtc -o MD.xtc", you will 
get one xtc data.

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of shiva birgani [sh.birg...@gmail.com]
Sent: Monday, December 06, 2010 3:16 PM
To: gmx-users
Subject: [gmx-users] Crashed run

Dear Justin
I had a crashed run and continued it by tpbconv and mdrun. After that in order 
to analysis the results of new MD run I used of this command
trjcat -s md2.tpr -settime
But when I want to compute RMSD, DSSP, ... I do not know how I can put together 
the results of MD1 (crashed run) and MD2 (continued one) to have the 
homogeneous results.
Could you please help me in this regard?
thanks in advance
Shiva



CONFIDENTIALITY: This email is intended solely for the person(s) named and may 
be confidential and/or privileged. If you are not the intended recipient, 
please delete it, notify us and do not copy, use, or disclose its content. 
Thank you.

Towards A Sustainable Earth: Print Only When Necessary
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Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar)

[Gerrit Groenhof]

 Please check if your stand-alone mopac binary works properly. Also 
check if the mdrun binary is linked against the libmopac.a


Gerrit

Message: 2
Date: Mon, 6 Dec 2010 11:55:58 +0530 (IST)
From: vidhya sankar
Subject: [gmx-users] : MOPAC gromacs mdreun error (vidhya sankar)
To: gmx-users@gromacs.org
Message-ID:<157886.66733...@web95506.mail.in.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear Gerrit  sir,
Thank you for your previous reply i tried as u said with  -nt 1 
option in mdrun but still i have got hte following error when i run mdrun_d
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 2
QMlevel: PM3/STO-3G
Program mdrun_d, VERSION 4.5.3
Source code file: qmmm.c, line: 697
Fatal error:
Semi-empirical QM only supported with Mopac.
  but i configured gromacs properly with mopac. how to solve the problem
  is ther is any link that i have not made available ? i am expecting your 
worthfull reply thanks isn advance




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RE: [gmx-users] Crashed run

[Mark Abraham]

On 12/06/10, "Shi Wenxiong (Dr)"   wrote:
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> I think you can use the command "trjcat -f MD1.xtc MD2.xtc -o MD.xtc", you 
> will get one xtc data.
> 
> 
> 
> 


Indeed, or  circumvent the problem with appropriate use of mdrun -append


Mark

> 
> 
> 
> 
> 
> 
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
> Of shiva birgani [sh.birg...@gmail.com]
> 
> Sent: Monday, December 06, 2010 3:16 PM
> 
> To: gmx-users
> 
> Subject: [gmx-users] Crashed run
> 
> 
> 
> 
> 
> 
> 
> Dear Justin
> 
> I had a crashed run and continued it by tpbconv and mdrun. After that in 
> order to analysis the results of new MD run I used of this command
> 
> trjcat -s md2.tpr -settime 
> 
> But when I want to compute RMSD, DSSP, ... I do not know how I can put 
> together the results of MD1 (crashed run) and MD2 (continued one) to have the 
> homogeneous results.
> 
> Could you please help me in this regard?
> 
> thanks in advance
> 
> Shiva
> 
> 
> 
> 
> 
> 
> 
> 
> CONFIDENTIALITY: This email is intended solely for the person(s) named and 
> may be confidential and/or privileged. If you are not the intended recipient, 
> please delete it, notify us and do not copy, use, or disclose its
>  content. Thank you.
> 
> 
> 
> Towards A Sustainable Earth: Print Only When Necessary
> 
> 
> 
> 
> 
> 
> 
>
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