date:20110906




fancy2012 wrote:

  Dear gmx users,

Are there some tutorials on constant PH simulations using gromacs? How 
should I state my work? Right now I have no idea on it.




Interestingly enough, there is a page devoted to this topic on the Gromacs wiki:

http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation

-Justin


--

_Best wishes,_

_Qinghua Liao_

_Ph.D student of Tianjin University, China_



--


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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Antw: [gmx-users] constant PH simulations

Look for the pKa-constants of each part of your system (e.g. each amino-acid). 
Then you can check each protonation state and change it according to your
application in the force-field.

Emanuel

>>> fancy2012  06.09.11 13.01 Uhr >>>
 Dear gmx users,

Are there some tutorials on constant PH simulations using gromacs? How should I 
state my work? Right now I have no idea on it.

--
Best wishes,
Qinghua Liao
Ph.D student of Tianjin University, China



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[gmx-users] analysis tools

2011-09-06 Thread Namd Namd

Dear All,

I’m a new NAMD user and use NAMD and
VMD for simulations. I want to ask a question about trajectory analysis. I
examined the gromacs 4.5.4 tools for making analysis and decided to use some of
them for my NAMD output files. Is there a way to convert my namd output files
into gromacs 4.5.4 outputs and use gromacs 4.5.4  analysis tools ?

I will be very happy if you
inform me about this issue.

Thanks a lot.-- 
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Re: [gmx-users] analysis tools




Namd Namd wrote:

Dear All,

I’m a new NAMD user and use NAMD and VMD for simulations. I want to ask 
a question about trajectory analysis. I examined the gromacs 4.5.4 tools 
for making analysis and decided to use some of them for my NAMD output 
files. Is there a way to convert my namd output files into gromacs 4.5.4 
outputs and use gromacs 4.5.4  analysis tools ?


I will be very happy if you inform me about this issue.



Gromacs tools can read any trajectory format that VMD can read, provided you 
have the VMD libraries available.  That said, many analysis tools still require 
a .tpr file, which means you need a Gromacs topology of your system so you can 
assemble this input.


-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] constant PH simulations

2011-09-06 Thread João M . Damas

That is not considered constant-pH MD.

Follow Justin's suggestion.

Cheers,
João

On Tue, Sep 6, 2011 at 12:47 PM, Emanuel Peter <
emanuel.pe...@chemie.uni-regensburg.de> wrote:

>
> Look for the pKa-constants of each part of your system (e.g. each
> amino-acid).
> Then you can check each protonation state and change it according to your
> application in the force-field.
>
> Emanuel
>
> >>> fancy2012 ** 06.09.11 13.01 Uhr >>>
>   Dear gmx users,
>
> Are there some tutorials on constant PH simulations using gromacs? How
> should I state my work? Right now I have no idea on it.
>
> --
>
> *Best wishes,*
>
> *Qinghua Liao*
>
> *Ph.D student of Tianjin University, China*
> **
>
> --
> 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
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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[gmx-users] Constraints not working in pull code (sometimes, sometimes not)

2011-09-06 Thread chris . neale

Are you 100% sure that you have the correct index group for your large  
box? Did you use a .ndx file that you prepared as input to mdrun or  
did you rely on the creation of a standard group? If you relied on the  
creation of a standard group, can you please try again with the larger  
box and a .ndx file that you created (preferably the exact one that  
you used with g_dist) and supplied to mdrun?


If that doesn't fix the problem, then I'd consider filing a redmine issue.

Chris.

-- original message --


Dear all,

I have reported a week ago update about my troubles with octanol/water slab
and pulling simulations, where COM code starts to report a wrong distances
between centre-of-masses between two groups when bigger box (see bellow) is
used.

So far, smaller box cured our actual calculation problems, but I am still
curious why g_dist and pullx.xvg are giving so different values, when I
enlarge the simulation box?

Best wishes
Karel Berka

Original mail down there




Dear all,

We have tested more strange behavior of constraints from pull code for
calculation of free energy differences small molecule on DOPC membrane and
octanol slab.
As I have reported previously, while the errors in free energy differences
on DOPC were rather small, the errors on octanol were strangely high.

We have prepared smaller slabs (as Chris Neale suggested) of octanol with
comparable size of box and we have also tried to analyze the position of
centres either via pullx.xvg provided by pull code, but also by g_dist
utility and to our surprise, size matters. A lot.
(Same groups were used in mdp for pull and for g_dist analysis, only
distances in z-axis is shown)

DOPC, 128 molecules, box size 6.2 6.4 8.3 , position of small molecule on
the edge of membrane
Time(ps)   pullf.xvgdist.xvg
 0.00-0.12416-0.12436
 1.00-0.12416-0.12433
 2.00-0.12416-0.12428
 3.00-0.12416-0.12430
 4.00-0.12416-0.12430
 5.00-0.12416-0.12432
 6.00-0.12416-0.12434
 7.00-0.12416-0.12449
As can be seen, the variation of distances reported by these two programs is
not perfect, but it is rather ok with precision of about 0.001 nm.

Octanol, 957 molecules, box size 5.7 5.9 13.7, position is similar on the
edge of slab, errors in free energy profiles are mainly here.
Time(ps)pullf.xvgdist.xvg
 0.00-2.81855-3.41133
 1.00-2.81076-3.44213
 2.00-2.82005-3.27949
 3.00-2.81856-3.35097
 4.00-2.82016-3.50378
 5.00-2.81849-3.63261
 6.00-2.81855-3.60058
 7.00-2.81870-3.80251
 8.00-2.81859-3.32790
 9.00-2.81849-3.24329
10.00-2.81855-3.28394
21.00-2.81855-4.02524
Here, the distances reported by pull code and by g_dist are completely
different with differences in about 1 nm! Visual inspection in VMD says that
small molecule is highly mobile a actual distances are reported rightly by
g_dist program.
Strangely enough, when we put distance measured by g_dist as a start into
the pull code without guessing the distances, but this also did not worked,
since the molecule tried to be at some completely different position and the
simulation crashed as the molecule speeded up.

Octanol, 475 molecules, box size 5.5 5.5 9.5, position also on the edge of
the slab
Time(ps)  pullf.xvgdist.xvg
 0.00-0.49996-0.49989
 1.00-0.49996-0.49988
 2.00-0.49996-0.49981
 3.00-0.49996-0.49981
 4.00-0.49996-0.50001
 5.00-0.49996-0.49987
 6.00-0.49996-0.49986
 7.00-0.49996-0.49994
 8.00-0.49997-0.49988
 9.00-0.49996-0.49980
10.00-0.49996-0.49988
Smaller box cured miraculously the problem, since here the difference is
similarly small as in DOPC case.

However just to remind another ache we had with octanol slab, in case of
octanol, the size of box in xy plane had to be held constant as the box
narrowed thorough the whole simulation when in anisotropic NPT ensemble.

Why g_dist and pullx show so different results in large box, I still do not
understand. Any suggestions?
And possibly any suggestions whether our box narrowing in case of octanol is
common or do we have another devil hidden there?

Best wishes
--
Zdraví skoro zdravý
Karel "Krápník" Berka


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Re: [gmx-users] atom type OXT


On 6/09/2011 11:39 AM, Sweta Iyer wrote:

Hi all,

I have been trying to pdbgmx my protein to obtain the gro and top files as 
follows:

pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top -ter  -ignh

However, I get an error message that states:

Atom OXT in residue SER 29 was not found in rtp entry SER with 8 atoms
while sorting atoms


We don't know what termini you are choosing (or want), so it's hard to 
help. See also http://www.gromacs.org/Documentation/How-tos/Multiple_Chains


Mark



I figure from previous threads that many ppl have been facing the similar 
issue. I also happened to go through the discussion in the bugs page.
This is how my pdb file looks like. Where would i have to re name my oxygen 
atoms in order to fix this?

ATOM  1  N   LEU X   1  36.020  45.310   8.310  1 1 1.63 
-0.15
ATOM  2  CA  LEU X   1  36.400  43.890   8.240  2 1 2.03  
0.10
ATOM  3  CB  LEU X   1  37.910  43.930   7.990  6 1 1.99  
0.00
ATOM  4  CG  LEU X   1  38.320  44.530   6.640 16 1 2.03  
0.00
ATOM  5  CD1 LEU X   1  39.830  44.320   6.680 17 1 1.94  
0.00
ATOM  6  CD2 LEU X   1  37.710  43.760   5.470 17 1 1.94  
0.00
ATOM  7  C  LEU X   1  35.910  43.180   9.510  3 1 1.67 
 0.60
ATOM  8  O   LEU X   1  36.680  43.050  10.460  4 1 1.38 
-0.55
ATOM  9  N   GLY X   2  34.710  42.620   9.390  1 1 1.63 
-0.15
ATOM 10  CA  GLY X   2  33.850  42.050  10.440  5 1 1.99  
0.10
ATOM 11  C   GLY X   2  34.300  40.610  10.700  3 1 1.67  
0.60
ATOM 12  O   GLY X   2  33.470  39.700  10.770  4 1 1.38 
-0.55
ATOM 13  N   ASN X   3  35.500  40.620  11.270  1 1 1.63 
-0.15
ATOM 14  CA  ASN X   3  36.180  39.350  11.510  2 1 2.03  
0.10
ATOM 15  CB  ASN X   3  37.610  39.430  10.970  6 1 1.99  
0.00
ATOM 16  CG  ASN X   3  37.560  39.470   9.440 11 1 1.67  
0.55
ATOM 17  OD1 ASN X   3  36.740  38.900   8.720 11 1 1.38 
-0.55
ATOM 18  ND2 ASN X   3  38.500  40.150   8.800 11 1 1.63  
0.00
ATOM 19  C   ASN X   3  36.140  38.770  12.930  3 1 1.67  
0.60
ATOM 20  O   ASN X   3  37.200  38.510  13.500  4 1 1.38 
-0.55
ATOM 21  N   GLY X   4  34.910  38.860  13.410  1 1 1.63 
-0.15
ATOM 22  CA  GLY X   4  34.410  38.420  14.720  5 1 1.99  
0.10
ATOM 23  C   GLY X   4  34.630  36.920  14.890  3 1 1.67  
0.60
ATOM 24  O   GLY X   4  34.060  36.200  14.070  4 1 1.38 
-0.55
ATOM 25  N   PRO X   5  35.630  36.460  15.640  1 0 1.63 
-0.25
ATOM 26  CA  PRO X   5  36.100  35.070  15.570  2 1 2.03  
0.10
ATOM 27  CB  PRO X   5  37.580  35.090  15.950  6 1 1.99  
0.00
ATOM 28  CG  PRO X   5  37.700  36.360  16.780  6 1 1.99  
0.00
ATOM 29  CD  PRO X   5  36.510  37.270  16.500  6 1 1.99  
0.10
ATOM 30  C   PRO X   5  35.290  34.130  16.470  3 0 1.67  
0.60
ATOM 31  O   PRO X   5  35.300  34.320  17.690  4 0 1.38 
-0.55
ATOM 32  N   ILE X   6  34.630  33.150  15.870  1 1 1.63 
-0.15
ATOM 33  CA  ILE X   6  33.650  32.240  16.500  2 1 2.03  
0.10
ATOM 34  CB  ILE X   6  33.090  31.180  15.550  6 1 2.03  
0.00
ATOM 35  CG1 ILE X   6  32.320  31.810  14.400 16 1 1.99  
0.00
ATOM 36  CG2 ILE X   6  32.170  30.220  16.310 17 1 1.94  
0.00
ATOM 37  CD  ILE X   6  31.910  30.940  13.210 17 1 1.94  
0.00
ATOM 38  C   ILE X   6  34.280  31.620  17.750  3 0 1.67  
0.60
ATOM 39  O   ILE X   6  33.860  31.920  18.870  4 0 1.38 
-0.55
ATOM 40  N   LEU X   7  35.460  31.050  17.520  1 0 1.63 
-0.15
ATOM 41  CA  LEU X   7  36.260  30.330  18.520  2 0 2.03  
0.10
ATOM 42  CB  LEU X   7  37.480  29.600  17.970  6 1 1.99  
0.00
ATOM 43  CG  LEU X   7  37.050  28.470  17.030 16 1 2.03  
0.00
ATOM 44  CD1 LEU X   7  38.310  28.200  16.220 17 1 1.94  
0.00
ATOM 45  CD2 LEU X   7  36.700  27.200  17.810 17 1 1.94  
0.00
ATOM 46  C   LEU X   7  36.640  31.270  19.670  3 0 1.67  
0.60
ATOM 47  O   LEU X   7  36.630  30.820  20.820  4 0 1.38 
-0.55
ATOM 48  N   ASN X   8  36.880  32.550  19.390  1 0 1.63 
-0.15
ATOM 49  CA  ASN X   8  37.240  33.460  20.490  2 0 2.03  
0.10
ATOM 50  CB  ASN X   8  38.030  34.660  19.970  6 1 1.99  
0.00
ATOM 51  CG  ASN X   8  39.510  34.340

Antw: Re: [gmx-users] constant PH simulations

Could you just tell me smth. !
No forcefield on whole earth is able to reproduce the pH realistically
by H+.
You just can apply pH of your system through the protonation states
of each part in your system.

monkey.

>>> João M. Damas 06.09.11 14.22 Uhr >>>
That is not considered constant-pH MD.

Follow Justin's suggestion.

Cheers,
João

On Tue, Sep 6, 2011 at 12:47 PM, Emanuel Peter
 wrote:

Look for the pKa-constants of each part of your system (e.g. each amino-acid). 
Then you can check each protonation state and change it according to your
application in the force-field.

Emanuel

>>> fancy2012  06.09.11 13.01 Uhr >>>
 Dear gmx users,

Are there some tutorials on constant PH simulations using gromacs? How should I
state my work? Right now I have no idea on it.

--
Best wishes,
Qinghua Liao
Ph.D student of Tianjin University, China

--
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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613

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Re: Antw: Re: [gmx-users] constant PH simulations

Emanuel Peter wrote:

Could you just tell me smth. !
No forcefield on whole earth is able to reproduce the pH realistically
by H+.
You just can apply pH of your system through the protonation states
of each part in your system.

Constant protonation state and constant pH are different.  Gromacs does not have 
the capability of doing constant pH simulations since such algorithms (i.e. 
http://mmtsb.org/workshops/mmtsb-ctbp_workshop_2009/Tutorials/CPHMD/cphmd_tutorial.html) 
are not implemented.  One can make an argument that comparing protonation states 
can be useful (I've done it), but you cannot equate constant protonation with 
constant pH.

-Justin

monkey.

 >>> João M. Damas 06.09.11 14.22 Uhr >>>
That is not considered constant-pH MD.

Follow Justin's suggestion.

Cheers,
João

On Tue, Sep 6, 2011 at 12:47 PM, Emanuel Peter 
> wrote:

Look for the pKa-constants of each part of your system (e.g. each
amino-acid).
Then you can check each protonation state and change it according to
your
application in the force-field.

Emanuel

 >>> fancy2012 __ 06.09.11 13.01 Uhr >>>
  Dear gmx users,

Are there some tutorials on constant PH simulations using gromacs?
How should I state my work? Right now I have no idea on it.

--

_Best wishes,_

_Qinghua Liao_

_Ph.D student of Tianjin University, China_

__

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--
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613

--

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: Re: [gmx-users] constant PH simulations

2011-09-06 Thread João M . Damas

As Justin said, constant protonation != constant pH.

Constant-pH MD does not simulate H+, but allows changes in protonation
states during the MD simulation. There are different algorithms
to accomplish that.

Cheers,
João

On Tue, Sep 6, 2011 at 2:04 PM, Emanuel Peter <
emanuel.pe...@chemie.uni-regensburg.de> wrote:

> Could you just tell me smth. !
> No forcefield on whole earth is able to reproduce the pH realistically
> by H+.
> You just can apply pH of your system through the protonation states
> of each part in your system.
>
> monkey.
>
>
>
> >>> João M. Damas** 06.09.11 14.22 Uhr >>>
>
> That is not considered constant-pH MD.
>
> Follow Justin's suggestion.
>
> Cheers,
> João
>
> On Tue, Sep 6, 2011 at 12:47 PM, Emanuel Peter <
> emanuel.pe...@chemie.uni-regensburg.de> wrote:
>
>>
>> Look for the pKa-constants of each part of your system (e.g. each
>> amino-acid).
>> Then you can check each protonation state and change it according to your
>> application in the force-field.
>>
>> Emanuel
>>
>> >>> fancy2012 ** 06.09.11 13.01 Uhr >>>
>>   Dear gmx users,
>>
>> Are there some tutorials on constant PH simulations using gromacs? How
>> should I state my work? Right now I have no idea on it.
>>
>> --
>>
>> *Best wishes,*
>>
>> *Qinghua Liao*
>>
>> *Ph.D student of Tianjin University, China*
>> **
>>
>> --
>> 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
>>
>
>
>
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
>  **
>
> --
> 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!
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> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
-- 
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[gmx-users] Average no of hbonds

2011-09-06 Thread Steven Neumann

Dear Gromacs Users,

I am calculating hbonds between my 10 ligands and each residue... How does
Gromacs calculate average number of hbonds per timeframe?
Example:

for Glycine:
Av. num of hbonds/timeframe
0.96

To check whether that is correct I added all hbonds formed with Glycine
during my simulation time over 2000 (each 50ps) timeframes and I obtained
value: 2900. If you divide it by 2000 you will never get 0.96 obviously. How
does Gromacs calculate it?

Steven
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Re: Yan: [gmx-users] analysis tools

Namd Namd wrote:

Dear Justin,

Well , I think that I can do it , can't I ? I have gromacs 4.0.7 and VMD 
1.8.7 . how can I make analysis using NAMD output files with these 

You can't do it with 4.0.7, only the 4.5.x series has the capability to use VMD 
libraries.  Your first message said you had 4.5.4 available.

softwares ? Could you please give me more information about this 
procedure ? What should I do ? Also ıs there a way to get a .tpr file 
from namd top or psf files ?

Not directly.  You'd either have to write a script to convert the topology to 
the right format (probably a lot of work) or follow a Gromacs tutorial to create 
the topology for your system.

http://www.gromacs.org/Documentation/Tutorials

-Justin

Thanks in advance

*Kimden:* Justin A. Lemkul 
*Kime:* Namd Namd ; Discussion list for GROMACS users 

*Gönderildiği Tarih:* 6 Eylül 2011 15:17 Salı
*Konu:* Re: [gmx-users] analysis tools

Namd Namd wrote:
 > Dear All,
 >
 > I’m a new NAMD user and use NAMD and VMD for simulations. I want to 
ask a question about trajectory analysis. I examined the gromacs 4.5.4 
tools for making analysis and decided to use some of them for my NAMD 
output files. Is there a way to convert my namd output files into 
gromacs 4.5.4 outputs and use gromacs 4.5.4  analysis tools ?

 >
 > I will be very happy if you inform me about this issue.
 >

Gromacs tools can read any trajectory format that VMD can read, provided 
you have the VMD libraries available.  That said, many analysis tools 
still require a .tpr file, which means you need a Gromacs topology of 
your system so you can assemble this input.

-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

--

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] Average no of hbonds




Steven Neumann wrote:

Dear Gromacs Users,
 
I am calculating hbonds between my 10 ligands and each residue... How 
does Gromacs calculate average number of hbonds per timeframe?

Example:
 
for Glycine:

Av. num of hbonds/timeframe
0.96
 
To check whether that is correct I added all hbonds formed with Glycine 
during my simulation time over 2000 (each 50ps) timeframes and I 
obtained value: 2900. If you divide it by 2000 you will never get 0.96 
obviously. How does Gromacs calculate it?
 


Just as you've proposed, the total number of hydrogen bonds divided by the 
number of frames.  Your calculation must have gone awry somewhere.


-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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Antw: Re: Re: [gmx-users] constant PH simulations

The standard procedure of H+ interchange and transition states can be done 
through QM/MM.
Please give one reference according to the algorithms you have mentioned.

Cheers.

>>> João M. Damas 06.09.11 15.19 Uhr >>>
As Justin said, constant protonation != constant pH.

Constant-pH MD does not simulate H+, but allows changes in protonation states
during the MD simulation. There are different algorithms to accomplish that.

Cheers,
João

On Tue, Sep 6, 2011 at 2:04 PM, Emanuel Peter
 wrote:
Could you just tell me smth. !
No forcefield on whole earth is able to reproduce the pH realistically
by H+.
You just can apply pH of your system through the protonation states
of each part in your system.

monkey.

>>> João M. Damas 06.09.11 14.22 Uhr >>>

That is not considered constant-pH MD.

Follow Justin's suggestion.

Cheers,
João

On Tue, Sep 6, 2011 at 12:47 PM, Emanuel Peter
 wrote:

Look for the pKa-constants of each part of your system (e.g. each amino-acid). 
Then you can check each protonation state and change it according to your
application in the force-field.

Emanuel

>>> fancy2012  06.09.11 13.01 Uhr >>>
 Dear gmx users,

Are there some tutorials on constant PH simulations using gromacs? How should I
state my work? Right now I have no idea on it.

--
Best wishes,
Qinghua Liao
Ph.D student of Tianjin University, China

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ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613

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Tel:+351-214469613

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Re: [gmx-users] Average no of hbonds


On 6/09/2011 11:37 PM, Steven Neumann wrote:

Dear Gromacs Users,
I am calculating hbonds between my 10 ligands and each residue... How 
does Gromacs calculate average number of hbonds per timeframe?

Example:
for Glycine:
Av. num of hbonds/timeframe
0.96
To check whether that is correct I added all hbonds formed with 
Glycine during my simulation time over 2000 (each 50ps) timeframes and 
I obtained value: 2900. If you divide it by 2000 you will never get 
0.96 obviously. How does Gromacs calculate it?


Presumably by adding up the number in each time frame and dividing by 
the number. Unless you have a highly-exposed glycine, forming more than 
one H-bond seems unlikely, and your 2900 number suggests it's happening 
lots of times. I expect you're comparing a sum of oranges with a sum of 
apples, but without more information about what you're doing in your 
attempt to check, we can't help much. Please be sure to read g_hbond -h, 
and the legends of any .xvg files you're looking at.


Mark
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Re: Antw: Re: Re: [gmx-users] constant PH simulations

Emanuel Peter wrote:

The standard procedure of H+ interchange and transition states can be done
through QM/MM.
Please give one reference according to the algorithms you have mentioned.

There are several cited at:

http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation

-Justin

Cheers.

 >>> João M. Damas 06.09.11 15.19 Uhr >>>
As Justin said, constant protonation != constant pH.

Constant-pH MD does not simulate H+, but allows changes in protonation 
states during the MD simulation. There are different algorithms 
to accomplish that.

Cheers,
João

On Tue, Sep 6, 2011 at 2:04 PM, Emanuel Peter 
> wrote:

Could you just tell me smth. !
No forcefield on whole earth is able to reproduce the pH realistically
by H+.
You just can apply pH of your system through the protonation states
of each part in your system.

monkey.

 >>> João M. Damas__ 06.09.11 14.22 Uhr >>>

That is not considered constant-pH MD.

Follow Justin's suggestion.

Cheers,
João

On Tue, Sep 6, 2011 at 12:47 PM, Emanuel Peter
mailto:emanuel.pe...@chemie.uni-regensburg.de>> wrote:

Look for the pKa-constants of each part of your system (e.g.
each amino-acid).
Then you can check each protonation state and change it
according to your
application in the force-field.

Emanuel

 >>> fancy2012 __ 06.09.11 13.01 Uhr >>>
  Dear gmx users,

Are there some tutorials on constant PH simulations using
gromacs? How should I state my work? Right now I have no idea on it.

--

_Best wishes,_

_Qinghua Liao_

_Ph.D student of Tianjin University, China_

__

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Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613 
__

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Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613

--

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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] Average no of hbonds

2011-09-06 Thread Steven Neumann

On Tue, Sep 6, 2011 at 2:50 PM, Mark Abraham wrote:

>  On 6/09/2011 11:37 PM, Steven Neumann wrote:
>
>> Dear Gromacs Users,
>> I am calculating hbonds between my 10 ligands and each residue... How does
>> Gromacs calculate average number of hbonds per timeframe?
>> Example:
>> for Glycine:
>> Av. num of hbonds/timeframe
>> 0.96
>> To check whether that is correct I added all hbonds formed with Glycine
>> during my simulation time over 2000 (each 50ps) timeframes and I obtained
>> value: 2900. If you divide it by 2000 you will never get 0.96 obviously. How
>> does Gromacs calculate it?
>>
>
> Presumably by adding up the number in each time frame and dividing by the
> number. Unless you have a highly-exposed glycine, forming more than one
> H-bond seems unlikely, and your 2900 number suggests it's happening lots of
> times. I expect you're comparing a sum of oranges with a sum of apples, but
> without more information about what you're doing in your attempt to check,
> we can't help much. Please be sure to read g_hbond -h, and the legends of
> any .xvg files you're looking at.
>
> Mark
>  Thank you Justin and Mark,
>

Yes, just found the mistake... I added pairs within 3.5 A instead of hbonds
so the Gromacs calculation is correct. So the value is 0.96 for Glycine. So
in this case it is a strong interaction. Are there any criteria to assess
strenght of interactions or binding affinity for residues? Was it described
anywhere for each residue to specify these values with respect to possible
hbonds for each residue (e.g. Glycine - 3)?

Steven



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Re: [gmx-users] Average no of hbonds




Steven Neumann wrote:



On Tue, Sep 6, 2011 at 2:50 PM, Mark Abraham > wrote:


On 6/09/2011 11:37 PM, Steven Neumann wrote:

Dear Gromacs Users,
I am calculating hbonds between my 10 ligands and each
residue... How does Gromacs calculate average number of hbonds
per timeframe?
Example:
for Glycine:
Av. num of hbonds/timeframe
0.96
To check whether that is correct I added all hbonds formed with
Glycine during my simulation time over 2000 (each 50ps)
timeframes and I obtained value: 2900. If you divide it by 2000
you will never get 0.96 obviously. How does Gromacs calculate it?


Presumably by adding up the number in each time frame and dividing
by the number. Unless you have a highly-exposed glycine, forming
more than one H-bond seems unlikely, and your 2900 number suggests
it's happening lots of times. I expect you're comparing a sum of
oranges with a sum of apples, but without more information about
what you're doing in your attempt to check, we can't help much.
Please be sure to read g_hbond -h, and the legends of any .xvg files
you're looking at.

Mark
Thank you Justin and Mark,

 
Yes, just found the mistake... I added pairs within 3.5 A instead of 
hbonds so the Gromacs calculation is correct. So the value is 0.96 for 
Glycine. So in this case it is a strong interaction. Are there any 
criteria to assess strenght of interactions or binding affinity for 
residues? Was it described anywhere for each residue to specify these 
values with respect to possible hbonds for each residue (e.g. Glycine - 3)?
 


Binding affinity can be determined from free energy calculations, but for the 
case of multiple ligands this would be an incredibly complex calculation (or 
series of calculations, really).  You might be able to make some argument about 
occupancy of available hydrogen bonding sites.


-Justin


Steven
 
 

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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] Average no of hbonds

2011-09-06 Thread Steven Neumann

On Tue, Sep 6, 2011 at 3:09 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>
>>
>> On Tue, Sep 6, 2011 at 2:50 PM, Mark Abraham > mark.abra...@anu.edu.**au >> wrote:
>>
>>On 6/09/2011 11:37 PM, Steven Neumann wrote:
>>
>>Dear Gromacs Users,
>>I am calculating hbonds between my 10 ligands and each
>>residue... How does Gromacs calculate average number of hbonds
>>per timeframe?
>>Example:
>>for Glycine:
>>Av. num of hbonds/timeframe
>>0.96
>>To check whether that is correct I added all hbonds formed with
>>Glycine during my simulation time over 2000 (each 50ps)
>>timeframes and I obtained value: 2900. If you divide it by 2000
>>you will never get 0.96 obviously. How does Gromacs calculate it?
>>
>>
>>Presumably by adding up the number in each time frame and dividing
>>by the number. Unless you have a highly-exposed glycine, forming
>>more than one H-bond seems unlikely, and your 2900 number suggests
>>it's happening lots of times. I expect you're comparing a sum of
>>oranges with a sum of apples, but without more information about
>>what you're doing in your attempt to check, we can't help much.
>>Please be sure to read g_hbond -h, and the legends of any .xvg files
>>you're looking at.
>>
>>Mark
>>Thank you Justin and Mark,
>>
>>  Yes, just found the mistake... I added pairs within 3.5 A instead of
>> hbonds so the Gromacs calculation is correct. So the value is 0.96 for
>> Glycine. So in this case it is a strong interaction. Are there any criteria
>> to assess strenght of interactions or binding affinity for residues? Was it
>> described anywhere for each residue to specify these values with respect to
>> possible hbonds for each residue (e.g. Glycine - 3)?
>>
>>
>
> Binding affinity can be determined from free energy calculations, but for
> the case of multiple ligands this would be an incredibly complex calculation
> (or series of calculations, really).  You might be able to make some
> argument about occupancy of available hydrogen bonding sites.
>
> -Justin
>

So will it be possible to exteract one ligand which from my visualisation
occupy one residue with highest number of av. hbonds (others aggregate on
bounded or bind weaker) and then calculate free energy?

Steven

>  Steven
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users
>>
>> 
>> >
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>>
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>>.
>>
>>
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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] Average no of hbonds




Steven Neumann wrote:



On Tue, Sep 6, 2011 at 3:09 PM, Justin A. Lemkul > wrote:




Steven Neumann wrote:



On Tue, Sep 6, 2011 at 2:50 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>
>> wrote:

   On 6/09/2011 11:37 PM, Steven Neumann wrote:

   Dear Gromacs Users,
   I am calculating hbonds between my 10 ligands and each
   residue... How does Gromacs calculate average number of
hbonds
   per timeframe?
   Example:
   for Glycine:
   Av. num of hbonds/timeframe
   0.96
   To check whether that is correct I added all hbonds
formed with
   Glycine during my simulation time over 2000 (each 50ps)
   timeframes and I obtained value: 2900. If you divide it
by 2000
   you will never get 0.96 obviously. How does Gromacs
calculate it?


   Presumably by adding up the number in each time frame and
dividing
   by the number. Unless you have a highly-exposed glycine, forming
   more than one H-bond seems unlikely, and your 2900 number
suggests
   it's happening lots of times. I expect you're comparing a sum of
   oranges with a sum of apples, but without more information about
   what you're doing in your attempt to check, we can't help much.
   Please be sure to read g_hbond -h, and the legends of any
.xvg files
   you're looking at.

   Mark
   Thank you Justin and Mark,

 Yes, just found the mistake... I added pairs within 3.5 A
instead of hbonds so the Gromacs calculation is correct. So the
value is 0.96 for Glycine. So in this case it is a strong
interaction. Are there any criteria to assess strenght of
interactions or binding affinity for residues? Was it described
anywhere for each residue to specify these values with respect
to possible hbonds for each residue (e.g. Glycine - 3)?
 



Binding affinity can be determined from free energy calculations,
but for the case of multiple ligands this would be an incredibly
complex calculation (or series of calculations, really).  You might
be able to make some argument about occupancy of available hydrogen
bonding sites.

-Justin

 
So will it be possible to exteract one ligand which from my 
visualisation occupy one residue with highest number of av. hbonds 
(others aggregate on bounded or bind weaker) and then calculate free energy?
 


Something like that might be possible, by calculating free energies over an MD 
rerun, but I've never tried it so I won't speculate.  Consult the literature for 
precedent and procedure and have a look at the free energy tutorial on the 
Gromacs site to see if you can piece it all together.  It won't be a trivial 
exercise.


-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] A question about simulating a box of ethane in GROMACS

2011-09-06 Thread Phil (Yang) Song

Hi, all

I am learning GROMACS 4.5.1 recently and encountered a problem that puzzled
me for weeks. I am wondering if someone can help me with this.

Here is the problem: I was trying to perform a MD simulation for 216 ethane
molecules in a box. I have first generated a box of ethane with random
position and orientation. Then, I wanted to run a minimization for the box
of ethane to get rid of close contact of the randomly ethane molecules.
However, I have found that some of the ethane molecules laid on top of each
other after minimization and infinity forces were resulted.

Since my mdp file was successfully used to generate other type of molecules
such as acetylene and ethylene and they should be correct. Also, I have
tried to use conjugate gradient instead of steepest decent for the
minimization, but this effort came out to be in vain.

Later, I thought the topology file should be the source of error. I have
carefully checked the topology file for couple of times but did not find any
obvious error. I have also tried to change the charges on each atom in the
ethane to 0 and then run the minimization. Again, the ethane was attracted
into each other. Hence, I think the vdw could be the problem. However, the
parameters of the vdw interaction are all from the opls-aa files that come
with gromacs and it should be fine.

Eventually, I am puzzled...

I am iterating the content of the content of mdp input file and itp file in
the email and also attaching the input and output of my result as a tarball.
Hope someone can help me to solve this problem.

Thank you in advance!

Best,
Phil Song


MDP file


; preprocessing options

; title of the simulation
title=

; include path
include  =

; cpp flag
define   =


; energy minimization
integrator= steep

; Start time and timestep in ps
tinit = 0
dt= 0.001
nsteps= 500

; run continuation or reperforming
init_step = 0

emtol = 1000.0
emstep= 0.01


; periodic boundary conditions
pbc   = xyz

periodic_molecules = no


; electrostatics and vdw options
; electrostatics method
coulombtype= PME
rcoulomb   = 1.3

; fourier setup for PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order  = 4
ewald_rtol = 1e-5
optimize_fft   = yes

ewald_geometry = 3d

; vdw cutoff
rvdw-switch= 0
rvdw   = 1.31


; neighbor list options
; neighbor list frequency
nstlist   = 10

; neighbor search algorithm
ns_type   = grid

; neighbor list cut-off
rlist = 1.30


; thermostat and barostat
tcoupl= v-rescale
tc_grps = System
ref_t = 50.5
tau_t = 0.5

pcoupl= berendsen
pcoupltype= isotropic
nstpcouple= 10
ref_p = 1.01325
tau_p = 1.0

; Using compressibility of ethanol at 273.1 (approximately)
; from J. Phys. Chem., 1963, 67 (10), pp 2160.2164

compressibility = 1.0e-5


; velocty generation
gen_vel   = yes
gen_temp  = 50.5
; gen_seed  = 173529


; output control options
; output frequency for coords, velocities and forces
nstxout   = 5000
nstvout   = 5000
nstfout   = 5000

; output frequency for energy
nstenergy = 5000
; energygrps=

; output frequency for log
nstlog= 5000

; output options for trajectory
nstxtcout = 5000
xtc_precision = 10
; xtc_grps  =



ITP file

; Ethane:
; Assign of the atom index
;
;  H2   H6
;  ||
; H3 - C1 - C5 - H7
;  ||
;  H4   H8
;

[ moleculetype ]
; namenrexcl
Ethane 3

[ atoms ]
;   nr  type   resnr   residuatomcgnr  charge  mass
 1  opls_135   1  ETH CE1  1-0.18
 2  opls_140   1  ETH HE2  1 0.06
 3  opls_140   1  ETH HE3  1 0.06
 4  opls_140   1  ETH HE4  1 0.06
 5  opls_135   1  ETH CE5  2-0.18
 6  opls_140   1  ETH HE6  2 0.06
 7  opls_140   1  ETH HE7  2 0.06
 8  opls_140   1  ETH HE8  2 0.06

[ bonds ]
;  ai  aj   funct c0c1
1   5   1
2   1   1
3   1   1
4   1   1
6   5   1
7   5   1
8   5   1

[ pairs ]
;  ai  aj   funct
2   6
2   7
2   8
3   6
3   7
3   8
4   6
4   7
4   8

[ angl

Re: [gmx-users] A question about simulating a box of ethane in GROMACS




Phil (Yang) Song wrote:

Hi, all

I am learning GROMACS 4.5.1 recently and encountered a problem that 
puzzled me for weeks. I am wondering if someone can help me with this.


Here is the problem: I was trying to perform a MD simulation for 216 
ethane molecules in a box. I have first generated a box of ethane with 
random position and orientation. Then, I wanted to run a minimization 
for the box of ethane to get rid of close contact of the randomly ethane 
molecules. However, I have found that some of the ethane molecules laid 
on top of each other after minimization and infinity forces were resulted.




Are they overlapping only after minimization, or does the starting configuration 
contain clashes?  Atoms should not be significantly displaced during EM, so I'd 
be inclined to believe the starting structure is the problem.


Since my mdp file was successfully used to generate other type of 
molecules such as acetylene and ethylene and they should be correct. 
Also, I have tried to use conjugate gradient instead of steepest decent 
for the minimization, but this effort came out to be in vain.


Later, I thought the topology file should be the source of error. I have 
carefully checked the topology file for couple of times but did not find 
any obvious error. I have also tried to change the charges on each atom 
in the ethane to 0 and then run the minimization. Again, the ethane was 
attracted into each other. Hence, I think the vdw could be the problem. 
However, the parameters of the vdw interaction are all from the opls-aa 
files that come with gromacs and it should be fine.




Simplify the system.  Rather than dealing with a full box of ethane, try 
minimizing one molecule, then a few (like 2 or 4) in a box, then build up.  If 
these small systems are stable, then the topology and .mdp are fine (though some 
of your cutoffs look strange to me).  Then build your target system once you've 
verified that all the pieces should be working together.


-Justin


Eventually, I am puzzled...

I am iterating the content of the content of mdp input file and itp file 
in the email and also attaching the input and output of my result as a 
tarball. Hope someone can help me to solve this problem.


Thank you in advance!

Best,
Phil Song


MDP file


; preprocessing options

; title of the simulation
title=

; include path
include  =

; cpp flag
define   =


; energy minimization
integrator= steep

; Start time and timestep in ps
tinit = 0
dt= 0.001
nsteps= 500

; run continuation or reperforming
init_step = 0

emtol = 1000.0
emstep= 0.01


; periodic boundary conditions
pbc   = xyz

periodic_molecules = no


; electrostatics and vdw options
; electrostatics method
coulombtype= PME
rcoulomb   = 1.3

; fourier setup for PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order  = 4
ewald_rtol = 1e-5
optimize_fft   = yes

ewald_geometry = 3d

; vdw cutoff
rvdw-switch= 0
rvdw   = 1.31


; neighbor list options
; neighbor list frequency
nstlist   = 10

; neighbor search algorithm
ns_type   = grid

; neighbor list cut-off
rlist = 1.30


; thermostat and barostat
tcoupl= v-rescale
tc_grps = System
ref_t = 50.5
tau_t = 0.5

pcoupl= berendsen
pcoupltype= isotropic
nstpcouple= 10
ref_p = 1.01325
tau_p = 1.0

; Using compressibility of ethanol at 273.1 (approximately)
; from J. Phys. Chem., 1963, 67 (10), pp 2160.2164

compressibility = 1.0e-5


; velocty generation
gen_vel   = yes
gen_temp  = 50.5
; gen_seed  = 173529


; output control options
; output frequency for coords, velocities and forces
nstxout   = 5000
nstvout   = 5000
nstfout   = 5000

; output frequency for energy
nstenergy = 5000
; energygrps=

; output frequency for log
nstlog= 5000

; output options for trajectory
nstxtcout = 5000
xtc_precision = 10
; xtc_grps  =



ITP file

; Ethane:
; Assign of the atom index
;
;  H2   H6
;  ||
; H3 - C1 - C5 - H7
;  ||
;  H4   H8
;

[ moleculetype ]
; namenrexcl
Ethane 3

[ atoms ]
;   nr  type   resnr   residuatomcgnr  charge  mass
 1  opls_135   1  ETH CE1  1-0.18
 2  opls_140   1  ETH HE2  1 0.06   
 3  opls

Re: [gmx-users] A question about simulating a box of ethane in GROMACS


On 7/09/2011 12:40 AM, Phil (Yang) Song wrote:

Hi, all

I am learning GROMACS 4.5.1 recently and encountered a problem that 
puzzled me for weeks. I am wondering if someone can help me with this.


Here is the problem: I was trying to perform a MD simulation for 216 
ethane molecules in a box. I have first generated a box of ethane with 
random position and orientation.


That's almost certainly inappropriate. Atomic clashes are inevitable, 
and EM will not fix severe problems.


Get a single molecule in a small box, and use genconf to replicate it. 
Then use EM and equilibrate thoroughly to remove the residual ordering. 
Judicious use of NPT will fix your density to whatever you want.


Mark

Then, I wanted to run a minimization for the box of ethane to get rid 
of close contact of the randomly ethane molecules. However, I have 
found that some of the ethane molecules laid on top of each other 
after minimization and infinity forces were resulted.


Since my mdp file was successfully used to generate other type of 
molecules such as acetylene and ethylene and they should be correct. 
Also, I have tried to use conjugate gradient instead of steepest 
decent for the minimization, but this effort came out to be in vain.


Later, I thought the topology file should be the source of error. I 
have carefully checked the topology file for couple of times but did 
not find any obvious error. I have also tried to change the charges on 
each atom in the ethane to 0 and then run the minimization. Again, the 
ethane was attracted into each other. Hence, I think the vdw could be 
the problem. However, the parameters of the vdw interaction are all 
from the opls-aa files that come with gromacs and it should be fine.


Eventually, I am puzzled...

I am iterating the content of the content of mdp input file and itp 
file in the email and also attaching the input and output of my result 
as a tarball. Hope someone can help me to solve this problem.


Thank you in advance!

Best,
Phil Song


MDP file


; preprocessing options

; title of the simulation
title=

; include path
include  =

; cpp flag
define   =


; energy minimization
integrator= steep

; Start time and timestep in ps
tinit = 0
dt= 0.001
nsteps= 500

; run continuation or reperforming
init_step = 0

emtol = 1000.0
emstep= 0.01


; periodic boundary conditions
pbc   = xyz

periodic_molecules = no


; electrostatics and vdw options
; electrostatics method
coulombtype= PME
rcoulomb   = 1.3

; fourier setup for PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order  = 4
ewald_rtol = 1e-5
optimize_fft   = yes

ewald_geometry = 3d

; vdw cutoff
rvdw-switch= 0
rvdw   = 1.31


; neighbor list options
; neighbor list frequency
nstlist   = 10

; neighbor search algorithm
ns_type   = grid

; neighbor list cut-off
rlist = 1.30


; thermostat and barostat
tcoupl= v-rescale
tc_grps = System
ref_t = 50.5
tau_t = 0.5

pcoupl= berendsen
pcoupltype= isotropic
nstpcouple= 10
ref_p = 1.01325
tau_p = 1.0

; Using compressibility of ethanol at 273.1 (approximately)
; from J. Phys. Chem., 1963, 67 (10), pp 2160.2164

compressibility = 1.0e-5


; velocty generation
gen_vel   = yes
gen_temp  = 50.5
; gen_seed  = 173529


; output control options
; output frequency for coords, velocities and forces
nstxout   = 5000
nstvout   = 5000
nstfout   = 5000

; output frequency for energy
nstenergy = 5000
; energygrps=

; output frequency for log
nstlog= 5000

; output options for trajectory
nstxtcout = 5000
xtc_precision = 10
; xtc_grps  =



ITP file

; Ethane:
; Assign of the atom index
;
;  H2   H6
;  ||
; H3 - C1 - C5 - H7
;  ||
;  H4   H8
;

[ moleculetype ]
; namenrexcl
Ethane 3

[ atoms ]
;   nr  type   resnr   residuatomcgnr  charge  
mass

 1  opls_135   1  ETH CE1  1-0.18
 2  opls_140   1  ETH HE2  1 0.06
 3  opls_140   1  ETH HE3  1 0.06
 4  opls_140   1  ETH HE4  1 0.06
 5  opls_135   1  ETH CE5  2-0.18
 6  opls_140   1  ETH HE6  2 0.06
 7  opls_140   1  ETH

Antw: Re: Re: [gmx-users] constant PH simulations (Emanuel Peter)

2011-09-06 Thread Gerrit Groenhof

> 
>   2. Antw: Re: Re: [gmx-users] constant PH simulations (Emanuel Peter)
>   
> Message: 2
> Date: Tue, 06 Sep 2011 15:49:28 +0200
> From: "Emanuel Peter" 
> Subject: Antw: Re: Re: [gmx-users] constant PH simulations
> To: 
> Message-ID: <4e66410802f100014...@gwsmtp1.uni-regensburg.de>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> The standard procedure of H+ interchange and transition states can be done 
> through QM/MM.
> Please give one reference according to the algorithms you have mentioned.

Please check Donnini et al, JCTC 7 (2011), 1962-1978.and the references therein.

have a banana,

Gerrit

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Re: Antw: Re: Re: [gmx-users] constant PH simulations

2011-09-06 Thread João Henriques

"No forcefield on whole earth is able to reproduce the pH realistically
by H+.
You just can apply pH of your system through the protonation states
of each part in your system."

I guess someone has been living in a cave for the past decade or so...

Cheers,
-- 
João Henriques
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[gmx-users] Freezing secondary structure

2011-09-06 Thread seunghwan lee

Hi All,

I am trying to run simulations of a small protein with the backbone frozen, 
but not the side chains. It looks like neither position restraint run or 
defining freeze_group will work since these options will freeze atoms in 
space. I also noticed that I may define [dihedral_restraints] and
[distance_restraints], but I couldn't find something like [angle_restraints]. 
This approach sounds quite tedious as well. 

What is the best way to freeze the secondary structure (a-helix in my case) 
during simulations?

Thanks.

Seunghwan Lee

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Re: [gmx-users] Freezing secondary structure

seunghwan lee wrote:

Hi All,

I am trying to run simulations of a small protein with the backbone frozen,
but not the side chains. It looks like neither position restraint run or
defining freeze_group will work since these options will freeze atoms in
space. I also noticed that I may define [dihedral_restraints] and
[distance_restraints], but I couldn't find something like [angle_restraints]. This approach sounds quite tedious as well.

Angle restraints wouldn't fix secondary structure; dihedral restraints are more
suitable.

What is the best way to freeze the secondary structure (a-helix in my case)
during simulations?

http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints

I suppose an alternate would be to have genrestr generate a distance restraint
file for you, but complex distance restraints limit performance because there
are difficulties parallelizing such systems.

-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] Gromacs 4.6?

2011-09-06 Thread Matthew Lardy

Hi,

I am wondering when Gromacs will support OpenMM 3+ and my GPU
architecture (S2050C Teslas)?  I have been patiently waiting, and
still haven't seen a new version (and yes, I have pulled back a
development version from git).  Still getting this nonsensical error
from OpenMM2 and while OpenMM3 compiles I obviously get NaN's
everywhere on the S2050C's since it is inappropriate to link them
together.

Am I doomed to use Amber forever?  :)

[Sorry, I just love Gromacs and have been waiting for four months for
an update that would allow me to execute it on my rackmounted tesla
blades...]

Thanks in advance,
Matthew
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[gmx-users] missing parameters in auto-generated topology file?

2011-09-06 Thread Yun Shi

Hi all,

I used pdb2gmx and selected amber99sb for generation of itp files of a
normal peptide within GROMACS 4.5.4.

But I saw that all the bonds, angles, and dihedral parameters (c0, c1, c2
...) were not present in the itp file, while only funct is defined. It seems
the same thing happens with opls ff.

So I wonder if those parameters are automatically generated according to
corresponding atom types when implementing grompp? What would happen if I
have exotic species and some atomic sequences are not defined in the   [
angletypes ] or   [ dihedraltypes ] section of amber99sb.ff/ffboned.itp ?


In the other case, when I used amb2gmx.pl to convert glycam force
field-parametized prmtop file to gromacs top file, I saw something like:

[ dihedrals ]
;i  j   k  l func   C0  ...  C5
19   18   20   21 3 0.75312 2.25936 0.0
-3.01248 0.0 0.0 ;
41   118   19 3 0.20920 0.62760 0.0
-0.83680 0.0 0.0 ;



Although I understand '3' in the fifth column indicates a
Ryckaert-Bellemans-potential function, but what parameters are those numbers
followed (0.75312 2.25936 0.0-3.01248 0.0
0.0) correspond to?

Thanks for any help!

Yun
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Re: [gmx-users] missing parameters in auto-generated topology file?




Yun Shi wrote:

Hi all,

I used pdb2gmx and selected amber99sb for generation of itp files of a 
normal peptide within GROMACS 4.5.4.


But I saw that all the bonds, angles, and dihedral parameters (c0, c1, 
c2 ...) were not present in the itp file, while only funct is defined. 
It seems the same thing happens with opls ff.


So I wonder if those parameters are automatically generated according to 
corresponding atom types when implementing grompp? What would happen if 


Yes, they're read from ffnonbonded.itp.

I have exotic species and some atomic sequences are not defined in the   
[ angletypes ] or   [ dihedraltypes ] section of amber99sb.ff/ffboned.itp ?




You'd get a fatal error that there are no default bonded types for those 
interactions.




In the other case, when I used amb2gmx.pl  to convert 
glycam force field-parametized prmtop file to gromacs top file, I saw 
something like:


[ dihedrals ]
;i  j   k  l func   C0  ...  C5
19   18   20   21 3 0.75312 2.25936 0.0
-3.01248 0.0 0.0 ;
41   118   19 3 0.20920 0.62760 0.0
-0.83680 0.0 0.0 ;




Although I understand '3' in the fifth column indicates a 
Ryckaert-Bellemans-potential function, but what parameters are those 
numbers followed (0.75312 2.25936 0.0-3.01248 
0.0 0.0) correspond to?




Please see manual section 4.2.12 and the table therein pertaining to 
Ryckaert-Bellemans dihedral coefficients.


-Justin


Thanks for any help!

Yun



--


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] energy terms vs. temperature

2011-09-06 Thread Juliette N.

Dear users,

I have a short question about temperature dependence of enregy terms i.e
bonds, angles, torsions, vdw , electorstatics. I am curious why these
energies increase with T. Especially bonded terms that have no temperature
dependence in the functional form ( force constants), why all bonded energy
terms are increasing with T?

Thanks for you comments,
J.
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Re: [gmx-users] energy terms vs. temperature




Juliette N. wrote:

Dear users,

I have a short question about temperature dependence of enregy terms i.e 
bonds, angles, torsions, vdw , electorstatics. I am curious why these 
energies increase with T. Especially bonded terms that have no 
temperature dependence in the functional form ( force constants), why 
all bonded energy terms are increasing with T?




I assume you're not using constraints?  Higher temperature induces bond 
excitation.  Atoms move faster with increasing T, hence kinetic energy influencs 
bonded terms.


-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] A question about simulating a box of ethane in GROMACS

2011-09-06 Thread Phil (Yang) Song

Hi,

Thank everyone for your suggestions.

I have tried to put less molecule in a small box and find this works!
Eventually I have solve the problem by using a larger initial box size for
the random generated position and orientation. It seemed that the overall
interaction of OPLS-AA between ethanes is attractive rather than repulsive,
which leads to atomic clashes...

The original box size was calculated from experimental density but
apparently this does not work for the OPLS-AA. I had used larger initial box
size previously (20% larger than experimental calculated box size) but it
did not work out and then I gave up on this direction. Now, I have tried to
enlarge the box size by 40% and everything works!

Finally I should offer my gratitude to all of you. Thank you!

Best,
Phil

On Tue, Sep 6, 2011 at 10:59 AM, Mark Abraham wrote:

>  On 7/09/2011 12:40 AM, Phil (Yang) Song wrote:
>
>   Hi, all
>
> I am learning GROMACS 4.5.1 recently and encountered a problem that puzzled
> me for weeks. I am wondering if someone can help me with this.
>
> Here is the problem: I was trying to perform a MD simulation for 216 ethane
> molecules in a box. I have first generated a box of ethane with random
> position and orientation.
>
>
> That's almost certainly inappropriate. Atomic clashes are inevitable, and
> EM will not fix severe problems.
>
> Get a single molecule in a small box, and use genconf to replicate it. Then
> use EM and equilibrate thoroughly to remove the residual ordering. Judicious
> use of NPT will fix your density to whatever you want.
>
> Mark
>
>
>Then, I wanted to run a minimization for the box of ethane to get rid
> of close contact of the randomly ethane molecules. However, I have found
> that some of the ethane molecules laid on top of each other after
> minimization and infinity forces were resulted.
>
> Since my mdp file was successfully used to generate other type of molecules
> such as acetylene and ethylene and they should be correct. Also, I have
> tried to use conjugate gradient instead of steepest decent for the
> minimization, but this effort came out to be in vain.
>
> Later, I thought the topology file should be the source of error. I have
> carefully checked the topology file for couple of times but did not find any
> obvious error. I have also tried to change the charges on each atom in the
> ethane to 0 and then run the minimization. Again, the ethane was attracted
> into each other. Hence, I think the vdw could be the problem. However, the
> parameters of the vdw interaction are all from the opls-aa files that come
> with gromacs and it should be fine.
>
> Eventually, I am puzzled...
>
> I am iterating the content of the content of mdp input file and itp file in
> the email and also attaching the input and output of my result as a tarball.
> Hope someone can help me to solve this problem.
>
> Thank you in advance!
>
> Best,
> Phil Song
>
>
> 
> MDP file
>
> 
> ; preprocessing options
>
> ; title of the simulation
> title=
>
> ; include path
> include  =
>
> ; cpp flag
> define   =
>
> 
> ; energy minimization
> integrator= steep
>
> ; Start time and timestep in ps
> tinit = 0
> dt= 0.001
> nsteps= 500
>
> ; run continuation or reperforming
> init_step = 0
>
> emtol = 1000.0
> emstep= 0.01
>
> 
> ; periodic boundary conditions
> pbc   = xyz
>
> periodic_molecules = no
>
> 
> ; electrostatics and vdw options
> ; electrostatics method
> coulombtype= PME
> rcoulomb   = 1.3
>
> ; fourier setup for PME
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order  = 4
> ewald_rtol = 1e-5
> optimize_fft   = yes
>
> ewald_geometry = 3d
>
> ; vdw cutoff
> rvdw-switch= 0
> rvdw   = 1.31
>
> 
> ; neighbor list options
> ; neighbor list frequency
> nstlist   = 10
>
> ; neighbor search algorithm
> ns_type   = grid
>
> ; neighbor list cut-off
> rlist = 1.30
>
> 
> ; thermostat and barostat
> tcoupl= v-rescale
> tc_grps = System
> ref_t = 50.5
> tau_t = 0.5
>
> pcoupl= berendsen
> pcoupltype= isotropic
> nstpcouple= 10
> ref_p = 1.01325
> tau_p = 1.0
>
> ; Using compressibility of ethanol at 273.1 (approximately)
> ; from J. Phys. Chem., 1963, 67 (10), pp 2160.2164
>
> compressibility = 1.0e-5
>
> 
> ; velocty generation
> gen_vel   = yes
> gen_temp  = 50.5
> ; gen_seed  = 173529
>
> 
> ; output control options
> ; output frequency for coo

Re: [gmx-users] energy terms vs. temperature

2011-09-06 Thread Juliette N.

On 6 September 2011 15:03, Justin A. Lemkul  wrote:

>
>
> Juliette N. wrote:
>
>> Dear users,
>>
>> I have a short question about temperature dependence of enregy terms i.e
>> bonds, angles, torsions, vdw , electorstatics. I am curious why these
>> energies increase with T. Especially bonded terms that have no temperature
>> dependence in the functional form ( force constants), why all bonded energy
>> terms are increasing with T?
>>
>>
> I assume you're not using constraints?  Higher temperature induces bond
> excitation.  Atoms move faster with increasing T, hence kinetic energy
> influencs bonded terms.
>

Thank you. There are no constraints.  At high T atoms move faster but
can you please describe a little more why higher velocity leads to higher
non bonded energies between particles? As for bonded terms, is that correct
to say higher velocities is equivalent to larger deviations from equilibrium
state of bonds, angles and dihedrals leasing to higher potential energies?

Thanks,

>
> -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
>
> ==**==
> --
> 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/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
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-- 
Thanks,
J. N.
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Re: [gmx-users] energy terms vs. temperature




Juliette N. wrote:



On 6 September 2011 15:03, Justin A. Lemkul > wrote:




Juliette N. wrote:

Dear users,

I have a short question about temperature dependence of enregy
terms i.e bonds, angles, torsions, vdw , electorstatics. I am
curious why these energies increase with T. Especially bonded
terms that have no temperature dependence in the functional form
( force constants), why all bonded energy terms are increasing
with T?


I assume you're not using constraints?  Higher temperature induces
bond excitation.  Atoms move faster with increasing T, hence kinetic
energy influencs bonded terms.


Thank you. There are no constraints.  At high T atoms move faster 
but can you please describe a little more why higher velocity leads to 
higher non bonded energies between particles? As for bonded terms, is 


Probably because they are more likely to collide and/or come in closer contact.

that correct to say higher velocities is equivalent to larger deviations 
from equilibrium state of bonds, angles and dihedrals leasing to higher 
potential energies?




It's all about competing forces.  Atoms have higher kinetic energy at higher 
temperature and so they can move faster.  Bonds work in opposition to atoms 
moving apart, so yes, there is some larger degree of deviation at higher T.


-Justin


Thanks,


-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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--
Thanks,
J. N.



--


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] gbsa.itp problem

2011-09-06 Thread Yao Yao

Hi All,

when I grompp for energy minimization, I met the error like,

--

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
processing topology...
Opening library file /share/apps/gromacs407/share/gromacs/top/ffamber03.itp
Opening library file /share/apps/gromacs407/share/gromacs/top/ffnonbonded.itp

WARNING 1 [file ffnonbonded.itp, line 38]:
  Overriding atomtype NA

Opening library file /share/apps/gromacs407/share/gromacs/top/ffbonded.itp
Opening library file /share/apps/gromacs407/share/gromacs/top/gbsa.itp

ERROR 1 [file gbsa.itp, line 1]:
  Invalid directive implicit_genborn_params


---
Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 756

Fatal error:
Unknown bond_atomtype 0.172
---

Since in the version 4.0.7 there is no gbsa.itp, I simply copied the file with 
the same name from gmx 4.5-4 and introduced ffamber03 force field into 4.0.7.
I understand updating to 4.5.X will solve this problem, but for testing my QMMM 
semi-empirical implementation, I have to use gmx version 4.0.7, at least for 
now.
So I am wondering if there is any way I can solve it in 4.0.7.


Thanks,

Yao-- 
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Re: [gmx-users] gbsa.itp problem




Yao Yao wrote:

Hi All,

when I grompp for energy minimization, I met the error like,

--
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
processing topology...
Opening library file /share/apps/gromacs407/share/gromacs/top/ffamber03.itp
Opening library file 
/share/apps/gromacs407/share/gromacs/top/ffnonbonded.itp


WARNING 1 [file ffnonbonded.itp, line 38]:
  Overriding atomtype NA

Opening library file /share/apps/gromacs407/share/gromacs/top/ffbonded.itp
Opening library file /share/apps/gromacs407/share/gromacs/top/gbsa.itp

ERROR 1 [file gbsa.itp, line 1]:
  Invalid directive implicit_genborn_params


---
Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 756

Fatal error:
Unknown bond_atomtype 0.172
---

Since in the version 4.0.7 there is no gbsa.itp, I simply copied the 
file with the same name from gmx 4.5-4 and introduced ffamber03 force 
field into 4.0.7.
I understand updating to 4.5.X will solve this problem, but for testing 
my QMMM semi-empirical implementation, I have to use gmx version 4.0.7, 
at least for now.

So I am wondering if there is any way I can solve it in 4.0.7.



You can't do implicit solvent simulations with a version < 4.5.

-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] gbsa.itp problem

Yao Yao wrote:

Hi Justin,

Thanks for your reply. Is there a way I can use explicit water to get 
rid of the error?

Solvate as you would any normal system and don't try to use force field files 
from newer versions.

-Justin

Thanks,

Yao

*From:* Justin A. Lemkul 
*To:* Yao Yao ; Discussion list for GROMACS users 

*Sent:* Tuesday, September 6, 2011 2:42 PM
*Subject:* Re: [gmx-users] gbsa.itp problem

Yao Yao wrote:
 > Hi All,
 >
 > when I grompp for energy minimization, I met the error like,
 >
 > --
 > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
 > checking input for internal consistency...
 > processing topology...
 > Opening library file 
/share/apps/gromacs407/share/gromacs/top/ffamber03.itp
 > Opening library file 
/share/apps/gromacs407/share/gromacs/top/ffnonbonded.itp

 >
 > WARNING 1 [file ffnonbonded.itp, line 38]:
 >  Overriding atomtype NA
 >
 > Opening library file 
/share/apps/gromacs407/share/gromacs/top/ffbonded.itp

 > Opening library file /share/apps/gromacs407/share/gromacs/top/gbsa.itp
 >
 > ERROR 1 [file gbsa.itp, line 1]:
 >  Invalid directive implicit_genborn_params
 >
 >
 > ---
 > Program grompp, VERSION 4.0.7
 > Source code file: toppush.c, line: 756
 >
 > Fatal error:
 > Unknown bond_atomtype 0.172
 > ---
 >
 > Since in the version 4.0.7 there is no gbsa.itp, I simply copied the 
file with the same name from gmx 4.5-4 and introduced ffamber03 force 
field into 4.0.7.
 > I understand updating to 4.5.X will solve this problem, but for 
testing my QMMM semi-empirical implementation, I have to use gmx version 
4.0.7, at least for now.

 > So I am wondering if there is any way I can solve it in 4.0.7.
 >

You can't do implicit solvent simulations with a version < 4.5.

-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

--

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] gbsa.itp problem

2011-09-06 Thread Yao Yao

I mean if I still want to use the introduced amber03 ff, when I solvate it as 
normal, it asks for gbsa.itp,

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


--


So is there any other file I need to change?

thanks,

yao





From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Tuesday, September 6, 2011 3:21 PM
Subject: Re: [gmx-users] gbsa.itp problem



Yao Yao wrote:
> Hi Justin,
> 
> Thanks for your reply. Is there a way I can use explicit water to get rid of 
> the error?
> 

Solvate as you would any normal system and don't try to use force field files 
from newer versions.

-Justin

> Thanks,
> 
> Yao
> 
> 
> *From:* Justin A. Lemkul 
> *To:* Yao Yao ; Discussion list for GROMACS users 
> 
> *Sent:* Tuesday, September 6, 2011 2:42 PM
> *Subject:* Re: [gmx-users] gbsa.itp problem
> 
> 
> 
> Yao Yao wrote:
>  > Hi All,
>  >
>  > when I grompp for energy minimization, I met the error like,
>  >
>  > --
>  > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
>  > checking input for internal consistency...
>  > processing topology...
>  > Opening library file /share/apps/gromacs407/share/gromacs/top/ffamber03.itp
>  > Opening library file 
>/share/apps/gromacs407/share/gromacs/top/ffnonbonded.itp
>  >
>  > WARNING 1 [file ffnonbonded.itp, line 38]:
>  >  Overriding atomtype NA
>  >
>  > Opening library file /share/apps/gromacs407/share/gromacs/top/ffbonded.itp
>  > Opening library file /share/apps/gromacs407/share/gromacs/top/gbsa.itp
>  >
>  > ERROR 1 [file gbsa.itp, line 1]:
>  >  Invalid directive implicit_genborn_params
>  >
>  >
>  > ---
>  > Program grompp, VERSION 4.0.7
>  > Source code file: toppush.c, line: 756
>  >
>  > Fatal error:
>  > Unknown bond_atomtype 0.172
>  > ---
>  >
>  > Since in the version 4.0.7 there is no gbsa.itp, I simply copied the file 
>with the same name from gmx 4.5-4 and introduced ffamber03 force field into 
>4.0.7.
>  > I understand updating to 4.5.X will solve this problem, but for testing my 
>QMMM semi-empirical implementation, I have to use gmx version 4.0.7, at least 
>for now.
>  > So I am wondering if there is any way I can solve it in 4.0.7.
>  >
> 
> You can't do implicit solvent simulations with a version < 4.5.
> 
> -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
> 
> 
> 
> 

-- 

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] gbsa.itp problem

Yao Yao wrote:
I mean if I still want to use the introduced amber03 ff, when I solvate 
it as normal, it asks for gbsa.itp,

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

--

So is there any other file I need to change?

You're still using 4.5 force field files.  You need to be using the ones that 
came with 4.0.7 if you're using 4.0.7.

-Justin

thanks,

yao

*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Tuesday, September 6, 2011 3:21 PM
*Subject:* Re: [gmx-users] gbsa.itp problem

Yao Yao wrote:
 > Hi Justin,
 >
 > Thanks for your reply. Is there a way I can use explicit water to get 
rid of the error?

 >

Solvate as you would any normal system and don't try to use force field 
files from newer versions.

-Justin

 > Thanks,
 >
 > Yao
 >
 > 
 > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
 > *To:* Yao Yao mailto:ya...@ymail.com>>; Discussion 
list for GROMACS users >

 > *Sent:* Tuesday, September 6, 2011 2:42 PM
 > *Subject:* Re: [gmx-users] gbsa.itp problem
 >
 >
 >
 > Yao Yao wrote:
 >  > Hi All,
 >  >
 >  > when I grompp for energy minimization, I met the error like,
 >  >
 >  > --
 >  > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
 >  > checking input for internal consistency...
 >  > processing topology...
 >  > Opening library file 
/share/apps/gromacs407/share/gromacs/top/ffamber03.itp
 >  > Opening library file 
/share/apps/gromacs407/share/gromacs/top/ffnonbonded.itp

 >  >
 >  > WARNING 1 [file ffnonbonded.itp, line 38]:
 >  >  Overriding atomtype NA
 >  >
 >  > Opening library file 
/share/apps/gromacs407/share/gromacs/top/ffbonded.itp

 >  > Opening library file /share/apps/gromacs407/share/gromacs/top/gbsa.itp
 >  >
 >  > ERROR 1 [file gbsa.itp, line 1]:
 >  >  Invalid directive implicit_genborn_params
 >  >
 >  >
 >  > ---
 >  > Program grompp, VERSION 4.0.7
 >  > Source code file: toppush.c, line: 756
 >  >
 >  > Fatal error:
 >  > Unknown bond_atomtype 0.172
 >  > ---
 >  >
 >  > Since in the version 4.0.7 there is no gbsa.itp, I simply copied 
the file with the same name from gmx 4.5-4 and introduced ffamber03 
force field into 4.0.7.
 >  > I understand updating to 4.5.X will solve this problem, but for 
testing my QMMM semi-empirical implementation, I have to use gmx version 
4.0.7, at least for now.

 >  > So I am wondering if there is any way I can solve it in 4.0.7.
 >  >
 >
 > You can't do implicit solvent simulations with a version < 4.5.
 >
 > -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
 >
 > 
 >
 >

-- 

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 

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.

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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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[gmx-users] Re: energy terms vs. temperature

2011-09-06 Thread Dr. Vitaly V. Chaban

Hello Juliette:

If you observe such behavior, I would suggest just to decrease a
time-step. You should have the same energies at all temperatures.

The larger is a time-step, the larger is a deviation from the energy
minimum (bonded potentials). The larger is the deviation, the higher
energy/force arises in order to get back to the equilibrium.


-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA



> Dear users,
>
> I have a short question about temperature dependence of enregy terms i.e
> bonds, angles, torsions, vdw , electorstatics. I am curious why these
> energies increase with T. Especially bonded terms that have no temperature
> dependence in the functional form ( force constants), why all bonded energy
> terms are increasing with T?
>
> Thanks for you comments,
> J.
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Re: [gmx-users] Re: energy terms vs. temperature




Dr. Vitaly V. Chaban wrote:

Hello Juliette:

If you observe such behavior, I would suggest just to decrease a
time-step. You should have the same energies at all temperatures.

The larger is a time-step, the larger is a deviation from the energy
minimum (bonded potentials). The larger is the deviation, the higher
energy/force arises in order to get back to the equilibrium.




Shorter time steps may be necessary to maintain stability of the system and to 
conserve energy, certainly, but I don't understand your point about the energy 
being independent of temperature.  Increasing temperature should, in theory, 
lead to excited states for bonds so they should be of higher energy.  For NVE, 
temperature fluctuations and compensatory potential changes keep the energy 
constant, but at different temperatures, NVT and NPT ensembles will inherently 
have different energies (and techniques like REMD derive their usefulness in 
part from this fact).


A given system should have a constant total energy, but I would certainly expect 
a system run at 300 K to have a different total energy from one at 400 K.


-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] Re: energy terms vs. temperature

2011-09-06 Thread Juliette N.

On 6 September 2011 15:42, Dr. Vitaly V. Chaban  wrote:

> Hello Juliette:
>
> If you observe such behavior, I would suggest just to decrease a
> time-step. You should have the same energies at all temperatures.
>
> The larger is a time-step, the larger is a deviation from the energy
> minimum (bonded potentials). The larger is the deviation, the higher
> energy/force arises in order to get back to the equilibrium.
>
> Dear Dr. Chaban,

Thank you for your message. I am using 1 fs as time step (no pressure
coupling, only NVT). I have seen some other papers where polymer chain
bonded and nonbonded terms increase with T. I am a little confused why you
think this should not be the case.

Thanks,

> --
> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
> Univ. Rochester, Rochester, New York 14627-0216
> THE UNITED STATES OF AMERICA
>
>
>
> > Dear users,
> >
> > I have a short question about temperature dependence of enregy terms i.e
> > bonds, angles, torsions, vdw , electorstatics. I am curious why these
> > energies increase with T. Especially bonded terms that have no
> temperature
> > dependence in the functional form ( force constants), why all bonded
> energy
> > terms are increasing with T?
> >
> > Thanks for you comments,
> > J.
>



-- 
Thanks,
J. N.
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Re: [gmx-users] Re: energy terms vs. temperature

2011-09-06 Thread Dr. Vitaly V. Chaban

Justin, I was speaking only about the bonded (and presumably,
harmonic) potentials. Decreasing the time-step, as I mentioned, never
made the things worse.

Vitaly



On Tue, Sep 6, 2011 at 7:59 PM, Justin A. Lemkul  wrote:
>
>
> Dr. Vitaly V. Chaban wrote:
>>
>> Hello Juliette:
>>
>> If you observe such behavior, I would suggest just to decrease a
>> time-step. You should have the same energies at all temperatures.
>>
>> The larger is a time-step, the larger is a deviation from the energy
>> minimum (bonded potentials). The larger is the deviation, the higher
>> energy/force arises in order to get back to the equilibrium.
>>
>>
>
> Shorter time steps may be necessary to maintain stability of the system and
> to conserve energy, certainly, but I don't understand your point about the
> energy being independent of temperature.  Increasing temperature should, in
> theory, lead to excited states for bonds so they should be of higher energy.
>  For NVE, temperature fluctuations and compensatory potential changes keep
> the energy constant, but at different temperatures, NVT and NPT ensembles
> will inherently have different energies (and techniques like REMD derive
> their usefulness in part from this fact).
>
> A given system should have a constant total energy, but I would certainly
> expect a system run at 300 K to have a different total energy from one at
> 400 K.
>
> -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] Re: energy terms vs. temperature




Dr. Vitaly V. Chaban wrote:

Justin, I was speaking only about the bonded (and presumably,
harmonic) potentials. Decreasing the time-step, as I mentioned, never
made the things worse.



How is it that harmonic potentials are unaffected by temperature?  Thermal 
excitation of bonds is a real phenomenon.


-Justin


Vitaly



On Tue, Sep 6, 2011 at 7:59 PM, Justin A. Lemkul  wrote:


Dr. Vitaly V. Chaban wrote:

Hello Juliette:

If you observe such behavior, I would suggest just to decrease a
time-step. You should have the same energies at all temperatures.

The larger is a time-step, the larger is a deviation from the energy
minimum (bonded potentials). The larger is the deviation, the higher
energy/force arises in order to get back to the equilibrium.



Shorter time steps may be necessary to maintain stability of the system and
to conserve energy, certainly, but I don't understand your point about the
energy being independent of temperature.  Increasing temperature should, in
theory, lead to excited states for bonds so they should be of higher energy.
 For NVE, temperature fluctuations and compensatory potential changes keep
the energy constant, but at different temperatures, NVT and NPT ensembles
will inherently have different energies (and techniques like REMD derive
their usefulness in part from this fact).

A given system should have a constant total energy, but I would certainly
expect a system run at 300 K to have a different total energy from one at
400 K.

-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







--


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: Antw: Re: Re: [gmx-users] constant PH simulations


On 7/09/2011 3:53 AM, João Henriques wrote:

I guess someone has been living in a cave for the past decade or so...


Please keep contributions to the mailing list constructive :-) 
Everyone's been wrong before!


Mark
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Re: [gmx-users] energy terms vs. temperature


On 7/09/2011 5:01 AM, Juliette N. wrote:

Dear users,

I have a short question about temperature dependence of enregy terms 
i.e bonds, angles, torsions, vdw , electorstatics. I am curious why 
these energies increase with T. Especially bonded terms that have no 
temperature dependence in the functional form ( force constants), why 
all bonded energy terms are increasing with T?


See 
http://en.wikipedia.org/wiki/Equipartition_theorem#Potential_energy_and_harmonic_oscillators


Mark
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Re: [gmx-users] A question about simulating a box of ethane in GROMACS


On 7/09/2011 5:23 AM, Phil (Yang) Song wrote:

Hi,

Thank everyone for your suggestions.

I have tried to put less molecule in a small box and find this works! 
Eventually I have solve the problem by using a larger initial box size 
for the random generated position and orientation. It seemed that the 
overall interaction of OPLS-AA between ethanes is attractive rather 
than repulsive, which leads to atomic clashes...


Random positions and orientations are different from non-clashing random 
positions and orientations. If your random generation takes account of 
inter-molecular forces, then it's not random, and won't lead to atomic 
clashes. So there is something missing or wrong about your description.


Mark
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[gmx-users] Installation gromacs in Scientific Linux

2011-09-06 Thread Nathalia Garces

Hello,

The last 6 months I've been working with gromacs (4.5.3 and 4.5.4) in Ubuntu
(10.4) and it has worked fine. The problem started when I changed the linux
distribution to Scientific Linux (5.3)... I followed the same steps to
download/configure gromacs but something's wrong or missing because the
simulations that I had been running on UBUNTU crashed in SL.

The command I use is very simple:

* mdrun -v -s topol.tpr*

In Ubuntu the simulation ends fine but in SL the application starts to write
on prompt at early steps (around 100)

*Step XX, time 0.XX (ps)  LINCS WARNING*
*relative constraint deviation after LINCS:*
*rms XX, max XX (between atoms XX and XX)*
*bonds that rotated more than 30 degrees:*
*...*
*Wrote pdb files with previous and current coordinates*
*
*
Until the simulation ends (around 250) with a message of

*
Segmentation fault
*


I tried different ways to configure gromacs but none of them seems to
resolve the problem
1) ./configure --prefix=
make
make install

2) ./configure --with-fft=fftw3 --prefix=  --without-x
make
make install

3)./configure --program-suffix= --disable-float --prefix= --exec-prefix= --enable-all-static --with-fft=fftw3
--without-x
make
make install

Moreover, I downloaded the benchmark posted in the gromacs web page to test
the simulations with other ".tpr" files. I run the first simulation
(implicit solvent) in UBUNTU and worked OK but the one on SL crashed (around
step 460) with the first two options of configuration. The last
configuration enabled the simulation to run OK( I decided to stop it at 4000
steps)...
This bewilders me because the last configuration permitted the benchmark to
run OK but not my file. I don't think my file has an unstable system because
it works all right in UBUNTU (and also Debian!)


In addition, I upgraded my linux distribution to the latest SL 5.x release
but it didn't make any change!


I hope you can help me with some guide on how to proceed a GOOD instalation
in SL or to let me know what is my problem and what I am missing.


Thank you for four answer,

Nathalia Garces
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[gmx-users] Surface tension calculation of a bilayer with bilayer normal in y-direction

2011-09-06 Thread Shou-Chuang Yang

Dear gmx-users,

I am pretty confused about how to calculate the surface tension of a bilayer
which with its bilayer
normal in y-direction rather than z-direction (as the default).

How does the Surf*SurfTen option in g-energy work? Does it take z as a
default bilayer normal?
If so, how can I calculate the surface tension in my case?

What if I use g_energy to get Pxx, Pyy and Pzz, than calculate my surface
tension as:
gamma= (Pyy - (Pxx+Pzz)/2) * Lz
What exactly is the "Lz"? Is it the length of the bilayer normal or the
length of either box-x or box-z
(in my case are the bilayer plane).

I will be vary thankful if anyone would kindly help me or discuss it with
me.
Thank you for your precious time.

Joanne
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[gmx-users] 3D pressure profile of a bilayer

2011-09-06 Thread Shou-Chuang Yang

Dear gmx-users,

Could anyone help me with the calculation of 3D pressure profile in a
function of y?
I used the provided gromacs-4.0.2_localpressure for my calculatioin. It
calculate
the 3D pressure profile as a function of z (the default setting of bilayer
normal
is z-direction).

In my case, I have a bilayer which rotate at the first few nano second run
and remained normal to y-direction for the rest. How can I obtain a 3D
pressure analysis
along the y-direction?
I really appreciated your help!

Thanks,
Joanne
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[gmx-users] No addition of ions

2011-09-06 Thread aiswarya pawar

Hi Gromacs users,

Am running a MD simulation over a protein complex and before adding the
ions. we run a grompp option then we get result as model net charge as some
integer ie if +2.00. so we got to add 2 CL ions. But when i ran my protein
for grompp it didnt give me any net charge so am not able to add any ions.
is this correct??

Thanks,
Aiswarya
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Re: [gmx-users] No addition of ions


On 7/09/2011 4:14 PM, aiswarya pawar wrote:

Hi Gromacs users,

Am running a MD simulation over a protein complex and before adding 
the ions. we run a grompp option then we get result as model net 
charge as some integer ie if +2.00. so we got to add 2 CL ions. But 
when i ran my protein for grompp it didnt give me any net charge so am 
not able to add any ions. is this correct??


There is no need to neutralize something that is already neutral. 
Whether it should be neutral is a function of your termini and side 
chains, and only you can address that. Whether you might want 
charge-balanced ions in your aqueous phase is also something for you to 
consider.


Mark

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Re: [gmx-users] Installation gromacs in Scientific Linux

On 7/09/2011 1:01 PM, Nathalia Garces wrote:

Hello,

The last 6 months I've been working with gromacs (4.5.3 and 4.5.4) in
Ubuntu (10.4) and it has worked fine. The problem started when I
changed the linux distribution to Scientific Linux (5.3)... I followed
the same steps to download/configure gromacs but something's wrong or
missing because the simulations that I had been running on UBUNTU
crashed in SL.

Maybe you just got lucky. The success of poorly-conditioned numerical
integration procedures can vary with what the user ate for lunch. Well,
not quite, but you get the idea. :)

You can make a better assessment by transferring a fully equilibrated
.tpr from your working machine to your non-working machine and seeing
whether that runs.

The command I use is very simple:

/ mdrun -v -s topol.tpr/

In Ubuntu the simulation ends fine but in SL the application starts to
write on prompt at early steps (around 100)

/Step XX, time 0.XX (ps) LINCS WARNING/
/relative constraint deviation after LINCS:/
/rms XX, max XX (between atoms XX and XX)/
/bonds that rotated more than 30 degrees:/
/.../
//Wrote pdb files with previous and current coordinates//
/
/
Until the simulation ends (around 250) with a message of

/
Segmentation fault
/

I tried different ways to configure gromacs but none of them seems to
resolve the problem

1) ./configure --prefix=
make
make install

2) ./configure --with-fft=fftw3 --prefix= --without-x
make
make install

3)./configure --program-suffix= --disable-float --prefix=path> --exec-prefix= --enable-all-static --with-fft=fftw3
--without-x

make
make install

You will need an FFTW install with float/double precision matching that
of the GROMACS configure command.

Moreover, I downloaded the benchmark posted in the gromacs web page to
test the simulations with other ".tpr" files. I run the first
simulation (implicit solvent) in UBUNTU and worked OK but the one on
SL crashed (around step 460) with the first two options of
configuration. The last configuration enabled the simulation to run
OK( I decided to stop it at 4000 steps)...
This bewilders me because the last configuration permitted the
benchmark to run OK but not my file. I don't think my file has an
unstable system because it works all right in UBUNTU (and also Debian!)

One possibility is some kind of dynamic linking failure from all your
different installations. If you always install to a --prefix that you
can delete later, then you can be sure that this kind of problem cannot
occur when you are testing different installations.

In addition, I upgraded my linux distribution to the latest SL 5.x
release but it didn't make any change!

I hope you can help me with some guide on how to proceed a GOOD
instalation in SL or to let me know what is my problem and what I am
missing.

Be sure you are following all the advice on the installation page of the
GROMACS webpages.

Mark

Thank you for four answer,

Nathalia Garces

[gmx-users] Re: atom type OXT

2011-09-06 Thread Sweta Iyer


> Message: 4
> Date: Tue, 06 Sep 2011 22:35:09 +1000
> From: Mark Abraham 
> Subject: Re: [gmx-users] atom type OXT
> To: Discussion list for GROMACS users 
> Message-ID: <4e66137d.9040...@anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 6/09/2011 11:39 AM, Sweta Iyer wrote:
>> Hi all,
>>
>> I have been trying to pdbgmx my protein to obtain the gro and top files
>> as follows:
>>
>> pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top -ter  -ignh
>>
>> However, I get an error message that states:
>>
>> Atom OXT in residue SER 29 was not found in rtp entry SER with 8 atoms
>> while sorting atoms
>
> We don't know what termini you are choosing (or want), so it's hard to
> help. See also
> http://www.gromacs.org/Documentation/How-tos/Multiple_Chains
>
> Mark
>

Hi,

I chose NH3+ as the start terminus at the first residue which is leucine
and COO- as my end terminus which is also on a leucine residue, which is
when it says it cant recognize atom type OXT on my last leucine residue.


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Antw: Re: Re: [gmx-users] constant PH simulations (Emanuel Peter)