Re: [gmx-users] NaCl

[Justin A. Lemkul]

nishap.pa...@utoronto.ca wrote:
I believe the bonds are not defined in the OPLS-AA force field for NaCl. 
I know this might sound like a stupid question, but is there a way to 
determine the bond force constant (kb), I tried to look it up, but I 
couldn't find anything.




There may be information from solid-state crystals, but as far as an aqueous 
solution goes, Mark is quite right - this is not a relevant state for NaCl in 
water.  There is no appreciable quantity of un-ionized NaCl in water, so that's 
why you're probably going to find it difficult to find bond parameters that are 
compatible with OPLS-AA.


-Justin




Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:

Hello,

   I want to simulate a simple NaCl ion in water. I know the method 
 using genion which adds individual Na+ and Cl- ion, but I wish to  
simulate Na-Cl connected rather than free ions floating in water.  
When I ran the grompp command I got the error:

No default Bond types
So I am thinking, I need to add b0 and Kb values for NaCl? Is that 
correct?


I would really appreciate some help!


This really is a case where you can try it and see much faster than it
will take you to type the email asking for help :)

Presumably, if you want a bond, and there are not parameters for it
already built in, then yes, you need to actually define the bond.

-Justin



Thanks.

-Nisha P




--


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


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


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Re: [gmx-users] NaCl

[nishap . patel]

I believe the bonds are not defined in the OPLS-AA force field for  
NaCl. I know this might sound like a stupid question, but is there a  
way to determine the bond force constant (kb), I tried to look it up,  
but I couldn't find anything.




Quoting "Justin A. Lemkul" :




nishap.pa...@utoronto.ca wrote:

Hello,

   I want to simulate a simple NaCl ion in water. I know the method  
 using genion which adds individual Na+ and Cl- ion, but I wish to   
simulate Na-Cl connected rather than free ions floating in water.   
When I ran the grompp command I got the error:

No default Bond types
So I am thinking, I need to add b0 and Kb values for NaCl? Is that correct?

I would really appreciate some help!


This really is a case where you can try it and see much faster than it
will take you to type the email asking for help :)

Presumably, if you want a bond, and there are not parameters for it
already built in, then yes, you need to actually define the bond.

-Justin



Thanks.

-Nisha P




--


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] NaCl

[Mark Abraham]

- Original Message -
From: nishap.pa...@utoronto.ca
Date: Tuesday, August 17, 2010 3:56
Subject: [gmx-users] NaCl
To: gmx-users@gromacs.org

> Hello,
> 
> I want to simulate a simple NaCl ion in 

Well, technically not an ion. I reckon that even given Moore's Law will 
continue to hold, it will be infeasible for at least the next thousand years 
for you to simulate a large enough water box that the dissociation equilibrium 
of NaCl will actually have a single NaCl molecule present. :-) Thus even if you 
succeed in finding reasonable parameters, I can't see how your simulation could 
mean anything.

> water. I know the method using genion which adds individual Na+ 
> and Cl- ion, but I wish to simulate Na-Cl connected rather than 
> free ions floating in water. When I ran the grompp command I got 
> the error:
> No default Bond types
> So I am thinking, I need to add b0 and Kb values for NaCl? Is 
> that correct?

Yes, but that's a non-trivial process. See 
http://www.gromacs.org/Documentation/How-tos/Parameterization

Mark

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Re: [gmx-users] NaCl

[Justin A. Lemkul]

nishap.pa...@utoronto.ca wrote:

Hello,

I want to simulate a simple NaCl ion in water. I know the method 
using genion which adds individual Na+ and Cl- ion, but I wish to 
simulate Na-Cl connected rather than free ions floating in water. When I 
ran the grompp command I got the error:

No default Bond types
So I am thinking, I need to add b0 and Kb values for NaCl? Is that correct?

I would really appreciate some help!


This really is a case where you can try it and see much faster than it will take 
you to type the email asking for help :)


Presumably, if you want a bond, and there are not parameters for it already 
built in, then yes, you need to actually define the bond.


-Justin



Thanks.

-Nisha P




--


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] g_gyrate -p => the radii of gyration about the principal axes ?

[David van der Spoel]

On 2010-08-16 20.15, Chih-Ying Lin wrote:



HI
What is the math definition of the radii of gyration about the principal
axes in Gromacs?

  I use the command   g_gyrate -p

  For lysozyme ,   I got  =>
  0.922754 1.22249 1.25603

  but in some paper, the authors got
  => 0.660  0.833  0.991

  It is a quite difference.

 From David =>
"The difference seems to be a constant factor.
Gromacs computes
sqrt (sum m (r-r_com)^2 / sum m)
I'm pretty sure it says so in the manual."


1. so the different factor is  sum m ,  not sum_N,   right ?  (N= number
of atoms)


Yes, if you do not divide by the total mass you have the moments of 
inertia. Does this difference in definition explain it?




2. the choice of the principal axes of the protein molecule is a
standard process ?
 => I mean the principal axes of the protein molecule  is fixed,
right  ?

No, it depends on the conformation.


 => I mean the math of the principal axes of the protein molecule is
defined all over the world , right ?

Thank you
Lin






On 2010-08-14 23.49, Chih-Ying Lin wrote:




 Hi
 To Calculate the radii of gyration about the principal axes

 I use the command
 g_gyrate -p

 For lysozyme ,   I got  =>
 0.922754 1.22249 1.25603

 but in some paper, the authors got
 => 0.660  0.833  0.991

 It is a quite difference.

 what is the definition of the radii of gyration about the principal

axes  ?

 i have checked the Gromacs manual but see nothing there.


The difference seems to be a constant factor.
Gromacs computes
sqrt (sum m (r-r_com)^2 / sum m)
I'm pretty sure it says so in the manual.





 Thank you

 Lin








--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] g_gyrate -p => the radii of gyration about the principal axes ?

[Chih-Ying Lin]

HI
What is the math definition of the radii of gyration about the principal
axes in Gromacs?

 I use the command   g_gyrate -p

 For lysozyme ,   I got  =>
 0.922754 1.22249 1.25603

 but in some paper, the authors got
 => 0.660  0.833  0.991

 It is a quite difference.

>From David =>
"The difference seems to be a constant factor.
Gromacs computes
sqrt (sum m (r-r_com)^2 / sum m)
I'm pretty sure it says so in the manual."


1. so the different factor is   sum m ,  not sum_N,   right ?  (N= number of
atoms)
2. the choice of the principal axes of the protein molecule is a standard
process ?
=> I mean the principal axes of the protein molecule  is fixed, right  ?
=> I mean the math of the principal axes of the protein molecule is
defined all over the world , right ?

Thank you
Lin






On 2010-08-14 23.49, Chih-Ying Lin wrote:
>
>
>
> Hi
> To Calculate the radii of gyration about the principal axes
>
> I use the command
> g_gyrate -p
>
> For lysozyme ,   I got  =>
> 0.922754 1.22249 1.25603
>
> but in some paper, the authors got
> => 0.660  0.833  0.991
>
> It is a quite difference.
>
> what is the definition of the radii of gyration about the principal axes
 ?
> i have checked the Gromacs manual but see nothing there.

The difference seems to be a constant factor.
Gromacs computes
sqrt (sum m (r-r_com)^2 / sum m)
I'm pretty sure it says so in the manual.


>
>
> Thank you
>
> Lin
>
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[gmx-users] NaCl

[nishap . patel]

Hello,

I want to simulate a simple NaCl ion in water. I know the method  
using genion which adds individual Na+ and Cl- ion, but I wish to  
simulate Na-Cl connected rather than free ions floating in water. When  
I ran the grompp command I got the error:

No default Bond types
So I am thinking, I need to add b0 and Kb values for NaCl? Is that correct?

I would really appreciate some help!

Thanks.

-Nisha P


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Re: [gmx-users] pdb2gmx-4.5 treats DNA as protein (and fails)

[Maiki]

David van der Spoel wrote:
> On 2010-08-16 14.44, Maiki wrote:
>> David van der Spoel wrote:
>>> On 2010-08-16 12.34, Maiki wrote:
 So, anybody knows why it does that or how to deal with nucleic acids?
 I only saw one similar question asked recently (with different error)
 which was also left without answer.
>>> Not all force fields have complete support for DNA. Try Charmm.
>> I tried all the forces I got with gromacs and they all failed with
>> different errors (ok, amber worked, but I wanted to try gromos for some
>> reasons). For charmm the error was:
>>
>> "There is a dangling bond at at least one of the terminal ends and
>> the force field does not provide terminal entries or files. Edit a
>> .n.tdb and/or .c.tdb file."
>
> did you run with the -ter option and select none?
I did now, and it changed nothing for charmm.
To be more precise it died before even asking me for dna termini.
the last part of output is:

Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/aminoacids.r2b
Reading pfv-dna.pdb...
Read 738 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
There are 2 chains and 0 blocks of water and 17 residues with 738 atoms

  chain  #res #atoms
  1 'C'19392 
  2 'D'17346 

All occupancies are one
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/atomtypes.atp
Atomtype 1
Reading residue database... (charmm27)
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/aminoacids.rtp
Residue 41
Sorting it all out...
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/dna.rtp
Residue 53
Sorting it all out...
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/lipids.rtp
Residue 65
Sorting it all out...
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/rna.rtp
Residue 77
Sorting it all out...
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/aminoacids.hdb
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/lipids.hdb
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
Opening force field file
/home/maiki/share/gromacs/top/charmm27.ff/aminoacids.c.tdb

Back Off! I just backed up pfv.top to ./#pfv.top.10#
Processing chain 1 'C' (392 atoms, 19 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Identified residue DA1 as a starting terminus.
Identified residue DA19 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
No suitable end (N or 5') terminus found in database - assuming this
residue
is already in a terminus-specific form and skipping terminus selection.
No suitable end (C or 3') terminus found in database - assuming this
residue
is already in a terminus-specific form and skipping terminus selection.
---
Program pdb2gmx_d, VERSION 4.5-beta2
Source code file: pdb2top.c, line: 883

Fatal error:
There is a dangling bond at at least one of the terminal ends and
the force field does not provide terminal entries or files. Edit a
.n.tdb and/or .c.tdb file.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I removed chain A(protein) and hetatms, only left C and D of double DNA
helix.

>>
>> so, it looks that charmm also tries to find N- and C- termini (or I
>> don't understand the error message which is also more than possible)
>> Besides, gromos does recognise DNA base pairs (DTHY for thymine etc,
>> they are in ff files) and all its atoms, only in the end it asks this
>> stupid question 'where is my NH3+ group?' and fails...
>>
>> There may be something with my pdb format but that's what I got from
>> rcsb/pdb. Is there a canonical description of PDB format expected by ffs
>> in pdb2gmx so I could correct my input myself? (if it's going to help)
>>

 Maiki wrote:
> Hi,
>
> I'm trying to convert protein-DNA complex using pdb2gmx with
> gromos53a6.ff
>
> $ pdb2gmx -f del.pdb -o del.gro -p del.top -i del.itp -n del.ndx
> -ignh
>
> In gromacs version 4.5-beta2 the result is:
>
> Processing chain 3 'C' (516 atoms, 25 residues)
> There are 0 donors and 0 acceptors
> There are 0 hydrogen bonds
> Identified residue DT1 as a starting terminus.
> Identified residue DA25 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Warning: 'DT' not found in residue topology database, trying to use
> 'DTHY'
> Start terminus: NH3+
> Warning: 'DA' not found in residue topology database, trying to use
>>>

[gmx-users] OPLS parameter for heme

[Shabana Vohra]

Hi, 

I am looking for OPLS parameters for heme. Does anyone has the parameters and 
would be able to provide it?

Any help or suggestions would be appreciated.

Thanks
Shabana


---
Shabana Vohra
SBCB Unit,Department of Biochemistry
University of Oxford
email: shabana.vo...@bioch.ox.ac.uk--
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[gmx-users] Re: Running MD on a dimeric protein

[onetwo]

Hello,,

I am really thankful to Mark, Justin and XAvier for helping me to clear my 
doubts.
Reply by Mark is really explainatory. I got my doubts clear.

Regards

Note: Forwarded message attached

-- Original Message --

From: "onetwo "twoon...@rediffmail.com
To: gmx-users@gromacs.org
Subject: Running MD on a dimeric protein--- Begin Message ---
Hello Sir,

I am simulating a protein which is a homodimer, when I did pdb2gmx, it 
generated a topolgy file  in which there were two chain topologies for each 
chain as :  

; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"   

and in Compound section gave ;

Compound#mols
Protein_A   1
Protein_B   1

I want to ask that if it will consider the system as one or two different 
proteins.

Also in production MD phase, in md.mdp file I mentioned

Berendsen temperature coupling is on in two groups
Tcoupl  = V-rescale
tc-grps = Protein Non-Protein
tau_t   = 0.1 0.1
ref_t   = 300 300

I have this doubt that as I have given tc-grps as Protein and Non-Protein, so 
if "Protein" will consider both the chains of the protein or not.

Thanks in advance
Regards--- End Message ---
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Re: [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells

[XAvier Periole]

On Aug 16, 2010, at 1:33 PM, Anirban Ghosh wrote:

Thanks a lot XAvier for clarifying my doubt. You mean to say "-rdd"  
option with mdrun, right?

yes

And why does this curvature of the membrane occurs?

No idea!


Thanks a lot once again.

Regards,

Anirban

On Mon, Aug 16, 2010 at 3:53 PM, XAvier Periole   
wrote:


Although a bit worrying the curvature of your bilayer is not
responsible for the error message you are seeing.

to solve the problem you have to increase to use the -rrd option
(see manual for explanation). Typicaly a value of 1.4 to 1.6 should
be fine.


On Aug 16, 2010, at 12:16 PM, Anirban Ghosh wrote:

Hi ALL,

I have made a CGMD system with multiple copies of a single protein  
in bilayer, by replicating the monomer using genconf in the X-Y  
plane. After running CGMD for about 100 ns, I am getting the  
following error:



  Energies (kJ/mol)
  Bond   G96AngleProper Dih.  Improper Dih. 
LJ (SR)
   4.73694e+043.00928e+044.68451e+038.26028e+02
-1.29727e+06
  Coulomb (SR)  PotentialKinetic En.   Total Energy 
Temperature
  -7.97216e+03   -1.7e+062.24656e+05   -9.97613e+05 
3.21675e+02

 Pressure (bar)  Cons. rmsd ()
  -9.97540e+001.69233e-05


Not all bonded interactions have been properly assigned to the  
domain decomposition cells


A list of missing interactions:
   G96Angle of  28064 missing  1

Molecule type 'DSPC'
the first 10 missing interactions, except for exclusions:
   G96Angle atoms   10   11   12  global  5309  5310  5311

---
Program mdrun_mpi, VERSION 4.0.7
Source code file: domdec_top.c, line: 341

Fatal error:
1 of the 62352 bonded interactions could not be calculated because  
some atoms involved moved further apart than the multi-body cut-off  
distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see  
option -rdd, for pairs and tabulated bonds also see option -ddcheck



On visual inspection I found that the bilayer is becoming curved  
(image attached). In the .top file I have mentioned the different  
monomers of my system as:


--
[ system ]
PROT in DSPC Bilayer

[ molecules ]
Protein 1
DSPC104
W   1397
NA+ 0
CL- 4
Protein 1
DSPC104
W   1397
NA+0
CL- 4
-

How can I resolve this error? Any suggestion is welcome.

Regards,

Anirban
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[gmx-users] Running MD on a dimeric protein

[onetwo]

Hello Sir,

I am simulating a protein which is a homodimer, when I did pdb2gmx, it 
generated a topolgy file  in which there were two chain topologies for each 
chain as :  

; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"   

and in Compound section gave ;

Compound#mols
Protein_A   1
Protein_B   1

I want to ask that if it will consider the system as one or two different 
proteins.

Also in production MD phase, in md.mdp file I mentioned

Berendsen temperature coupling is on in two groups
Tcoupl  = V-rescale
tc-grps = Protein Non-Protein
tau_t   = 0.1 0.1
ref_t   = 300 300

I have this doubt that as I have given tc-grps as Protein and Non-Protein, so 
if "Protein" will consider both the chains of the protein or not.

Thanks in advance
Regards-- 
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Re: [gmx-users] Running MD on a dimeric protein

[Mark Abraham]

- Original Message -
From: onetwo  
Date: Monday, August 16, 2010 18:55
Subject: [gmx-users] Running MD on a dimeric protein
To: gmx-users@gromacs.org

> Hello Sir,
 > 
>  I am simulating a protein which is a homodimer, when I did pdb2gmx, it 
> generated a topolgy file  in which there were two chain topologies for each 
> chain as :  
 > 
>  ; Include chain topologies
>  #include "topol_A.itp"
>  #include "topol_B.itp"   
 > 
>  and in Compound section gave ;
 > 
>  Compound#mols
>  Protein_A   1
>  Protein_B   1
 > 
>  I want to ask that if it will consider the system as one or two different 
> proteins.
 > 
>  Also in production MD phase, in md.mdp file I mentioned
 > 
>  Berendsen temperature coupling is on in two groups
>  Tcoupl  = V-rescale
>  tc-grps = Protein Non-Protein
>  tau_t   = 0.1 0.1
>  ref_t   = 300 300
 > 
>  I have this doubt that as I have given tc-grps as Protein and Non-Protein, 
> so if "Protein" will consider both the chains of the protein or not.

 The GROMACS index groups (of which tc-grps are perhaps the most commonly used, 
see manual for more info) are either provided to grompp via a file supplied 
with the -n parameter, or (in its absence) automatically generated by grompp. 
Either way, its output should provide enough clues to work out what has been 
regarded as Protein (e.g. residue or atom count). In extremis, you can use 
gmxdump on the .tpr to see the contents of the groups.

Unless you've gone out of your way to break things (e.g. changed the database 
of amino acid atom names), the default index groups generated by grompp will 
regard both your dimer parts as Protein.

If the dimer parts are adjacent, then tc-grps of Protein and Non-Protein are 
probably best. If they're apart, then you may want to couple the two parts 
separately. See http://www.gromacs.org/Documentation/Terminology/Thermostats in 
the first instance.

Mark

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Re: [gmx-users] pdb2gmx-4.5 treats DNA as protein (and fails)

[David van der Spoel]

On 2010-08-16 14.44, Maiki wrote:

David van der Spoel wrote:

On 2010-08-16 12.34, Maiki wrote:

So, anybody knows why it does that or how to deal with nucleic acids?
I only saw one similar question asked recently (with different error)
which was also left without answer.

Not all force fields have complete support for DNA. Try Charmm.

I tried all the forces I got with gromacs and they all failed with
different errors (ok, amber worked, but I wanted to try gromos for some
reasons). For charmm the error was:

"There is a dangling bond at at least one of the terminal ends and
the force field does not provide terminal entries or files. Edit a
.n.tdb and/or .c.tdb file."


did you run with the -ter option and select none?


so, it looks that charmm also tries to find N- and C- termini (or I
don't understand the error message which is also more than possible)
Besides, gromos does recognise DNA base pairs (DTHY for thymine etc,
they are in ff files) and all its atoms, only in the end it asks this
stupid question 'where is my NH3+ group?' and fails...

There may be something with my pdb format but that's what I got from
rcsb/pdb. Is there a canonical description of PDB format expected by ffs
in pdb2gmx so I could correct my input myself? (if it's going to help)



Maiki wrote:

Hi,

I'm trying to convert protein-DNA complex using pdb2gmx with
gromos53a6.ff

$ pdb2gmx -f del.pdb -o del.gro -p del.top -i del.itp -n del.ndx -ignh

In gromacs version 4.5-beta2 the result is:

Processing chain 3 'C' (516 atoms, 25 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Identified residue DT1 as a starting terminus.
Identified residue DA25 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Warning: 'DT' not found in residue topology database, trying to use
'DTHY'
Start terminus: NH3+
Warning: 'DA' not found in residue topology database, trying to use
'DADE'
End terminus: COO-
Warning: 'DT' not found in residue topology database, trying to use
'DTHY'
Warning: 'DA' not found in residue topology database, trying to use
'DADE'
Warning: 'DG' not found in residue topology database, trying to use
'DGUA'
(...)
Warning: 'DA' not found in residue topology database, trying to use
'DADE'

---
Program pdb2gmx, VERSION 4.5-beta2
Source code file: pdb2top.c, line: 922

Fatal error:
atom N not found in buiding block 1DT while combining tdb and rtp
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
---












--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] pdb2gmx-4.5 treats DNA as protein (and fails)

[Maiki]

David van der Spoel wrote:
> On 2010-08-16 12.34, Maiki wrote:
>> So, anybody knows why it does that or how to deal with nucleic acids?
>> I only saw one similar question asked recently (with different error)
>> which was also left without answer.
> Not all force fields have complete support for DNA. Try Charmm.
I tried all the forces I got with gromacs and they all failed with
different errors (ok, amber worked, but I wanted to try gromos for some
reasons). For charmm the error was:

"There is a dangling bond at at least one of the terminal ends and
the force field does not provide terminal entries or files. Edit a
.n.tdb and/or .c.tdb file."

so, it looks that charmm also tries to find N- and C- termini (or I
don't understand the error message which is also more than possible)
Besides, gromos does recognise DNA base pairs (DTHY for thymine etc,
they are in ff files) and all its atoms, only in the end it asks this
stupid question 'where is my NH3+ group?' and fails...

There may be something with my pdb format but that's what I got from
rcsb/pdb. Is there a canonical description of PDB format expected by ffs
in pdb2gmx so I could correct my input myself? (if it's going to help)

>>
>> Maiki wrote:
>>> Hi,
>>>
>>> I'm trying to convert protein-DNA complex using pdb2gmx with
>>> gromos53a6.ff
>>>
>>> $ pdb2gmx -f del.pdb -o del.gro -p del.top -i del.itp -n del.ndx -ignh
>>>
>>> In gromacs version 4.5-beta2 the result is:
>>>
>>> Processing chain 3 'C' (516 atoms, 25 residues)
>>> There are 0 donors and 0 acceptors
>>> There are 0 hydrogen bonds
>>> Identified residue DT1 as a starting terminus.
>>> Identified residue DA25 as a ending terminus.
>>> 8 out of 8 lines of specbond.dat converted successfully
>>> Warning: 'DT' not found in residue topology database, trying to use
>>> 'DTHY'
>>> Start terminus: NH3+
>>> Warning: 'DA' not found in residue topology database, trying to use
>>> 'DADE'
>>> End terminus: COO-
>>> Warning: 'DT' not found in residue topology database, trying to use
>>> 'DTHY'
>>> Warning: 'DA' not found in residue topology database, trying to use
>>> 'DADE'
>>> Warning: 'DG' not found in residue topology database, trying to use
>>> 'DGUA'
>>> (...)
>>> Warning: 'DA' not found in residue topology database, trying to use
>>> 'DADE'
>>>
>>> ---
>>> Program pdb2gmx, VERSION 4.5-beta2
>>> Source code file: pdb2top.c, line: 922
>>>
>>> Fatal error:
>>> atom N not found in buiding block 1DT while combining tdb and rtp
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> ---
>>>
>>>
>>
>
>

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RE: [gmx-users] tpi segmentation fault

[Javier Cerezo]

Thanks a lot for your reply Dr. Hess.

As you expected, the -nt 1 option in the mdrun fix the problem in 
4.5-beta version. Actually, the problem there was not a "segmentation 
fault" warning appearing in the output, it just got stop in an 
apparently random behavior. With 4.0.7 version that I have compiled from 
source I still have the same "Segmentation fault" problem. I tried with 
a trajectory generated with the same compiled version but it still fails.


Anyway, I guess it can be due to a mistake during my compilation since 
this feature had no such failure reports in the mailing list, and in 
preliminary tries, it seems that the results for the tpi calculation in 
4.0.7 and 4.5beta versions are similar. Concretely, I am trying to use a 
modification of the tpi program similar to the slab-tpi proposed by 
Robert Vacha 
(http://lists.gromacs.org/pipermail/gmx-developers/2008-December/002931.html) 
but, for practical reasons the partition of the box is performed 
specifying the number of slices in which the box is partitioned 
(nslices) and in which partition the particle are inserted (islice). For 
that I just modified tpi.c (line 431) to:
   x_init[ZZ] = (gmx_rng_uniform_real(tpi_rand) + islice - 
1)*state->box[ZZ][ZZ]/nslices;


where nslice and islice are correctly passed to the program though 
unused mdp parameters in tpi calculations (nstxtcout and nstenergy). I 
applied it for the study of a lipid bilayer and as a results I expected 
a nice simmetrical curve for  vs. Z-positions (similar to the ones 
in J. Phys. Chem. B 2007, 111, 12748-12755) but I got rough irregular 
curves and partition dependent (the shape depends on nslices). I am 
using pseudo-NPT ensemble (Berendsen coupling) in the production step 
and nsteps=1 nstlist=100 for tpi insertion. I tried to use different 
versions to investigation why the results are not the expected ones. But 
maybe there is something wrong in the modification (for exmaple, I think 
that there might be some issues since the box size and subsequently the 
partitions are being modified during the trajectory). Does someone have 
any idea about that?


Thank you.

Javier




Date: Mon, 16 Aug 2010 11:49:21 +0200
From: Berk Hess
Subject: RE: [gmx-users] tpi segmentation fault
To: Discussion list for GROMACS users
Message-ID:
Content-Type: text/plain; charset="iso-8859-1"


Hi,

I don't understand why 4.0.7 gives a segv.

But 4.5-beta probably gives a segv because of a parallel problem.
Could you try 4.5-beta with the mdrun option -nt 1
and report back?

Thanks,

Berk

   

Date: Fri, 13 Aug 2010 18:35:55 +0200
From:j...@um.es
To:gmx-users@gromacs.org
Subject: [gmx-users] tpi segmentation fault

Hi all.

I am trying to perform a tpi (test particle insertion) calculation on a
trajectory generated with mpi_mdrun (gromacs 4.0.7, run in a Beowulf
cluster of Intel(R) Core(TM)2 Quad CPUQ6600  @ 2.40GHz). I am using
tpi integrator in the mdp file and the following command:

   $  grompp -f tpi.mdp -c 32hoa_128dmpcwrun.gro -n index_tpi.ndx -p
topol_tpi.top
   $  mdrun -rerun 32hoa_128dmpcwrun.trr -g tpi.log

I tried different versions of gromcas and for 4.0.X I got a segmentation
fault getting the message:

  trn version: GMX_trn_file (single precision)
  Reading frame   0 time0.000   Segmentation fault

using a compiled version with "config --prefix
/home/cerezo/Programs/gromacs4.07" + "make" + "make install". However,
it works when I used a precompiled version (got with apt-get, I have
kubuntu). So I guess that it may be due to a mistake during the
compilation. In addition, other integrators (i.e. md, steep) work
correctly with the version I've compiled. My system is and Intel(R)
Core(TM)2 Quad CPUQ8400  @ 2.66GHz. Is there any trick I could try
in the compilation?

I also tried gromacs-4.5-betaX and it works but sometimes (apparently
randomly) the calculation gets stops (as if it had entered in an
infinite loop) after reading the last frame.

Thanks for your attention!

Javier

--
Javier CEREZO BASTIDA
Estudiante de Doctorado
-
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434

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--
Javier CEREZO BASTIDA
Estudiante de Doctorado
-
Dpto. Química-Física
Universidad de Murc

Re: [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells

[Justin A. Lemkul]

Anirban Ghosh wrote:

Hi ALL,

I have made a CGMD system with multiple copies of a single protein in 
bilayer, by replicating the monomer using genconf in the X-Y plane. 
After running CGMD for about 100 ns, I am getting the following error:



   Energies (kJ/mol)
   Bond   G96AngleProper Dih.  Improper Dih.LJ (SR)
4.73694e+043.00928e+044.68451e+038.26028e+02   -1.29727e+06
   Coulomb (SR)  PotentialKinetic En.   Total EnergyTemperature
   -7.97216e+03   -1.7e+062.24656e+05   -9.97613e+053.21675e+02
 Pressure (bar)  Cons. rmsd ()
   -9.97540e+001.69233e-05


Not all bonded interactions have been properly assigned to the domain 
decomposition cells


A list of missing interactions:
G96Angle of  28064 missing  1

Molecule type 'DSPC'
the first 10 missing interactions, except for exclusions:
G96Angle atoms   10   11   12  global  5309  5310  5311

---
Program mdrun_mpi, VERSION 4.0.7
Source code file: domdec_top.c, line: 341

Fatal error:
1 of the 62352 bonded interactions could not be calculated because some 
atoms involved moved further apart than the multi-body cut-off distance 
(1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for 
pairs and tabulated bonds also see option -ddcheck



On visual inspection I found that the bilayer is becoming curved (image 
attached). In the .top file I have mentioned the different monomers of 
my system as:


--
[ system ]
PROT in DSPC Bilayer

[ molecules ]
Protein 1
DSPC104
W   1397
NA+ 0
CL- 4
Protein 1
DSPC104
W   1397
NA+0
CL- 4
-

How can I resolve this error? Any suggestion is welcome.



Search the list archive.  This error has come up before, and I know there's been 
at least one instance of it for a CG system.  I believe the answer was to 
increase -rdd (since bonded interactions occur at longer distance in CG 
systems), but please do the search for yourself.


-Justin


Regards,

Anirban





--


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] tpi segmentation fault

[Sander Pronk]

Hi Javier,

I've just committed a fix to the git 4.5 tree. Thanks for reporting this. 

Sander

On 13 Aug 2010, at 18:35 , Javier Cerezo wrote:

> Hi all.
> 
> I am trying to perform a tpi (test particle insertion) calculation on a 
> trajectory generated with mpi_mdrun (gromacs 4.0.7, run in a Beowulf cluster 
> of Intel(R) Core(TM)2 Quad CPUQ6600  @ 2.40GHz). I am using tpi 
> integrator in the mdp file and the following command:
> 
> $  grompp -f tpi.mdp -c 32hoa_128dmpcwrun.gro -n index_tpi.ndx -p 
> topol_tpi.top
> $  mdrun -rerun 32hoa_128dmpcwrun.trr -g tpi.log
> 
> I tried different versions of gromcas and for 4.0.X I got a segmentation 
> fault getting the message:
> 
>trn version: GMX_trn_file (single precision)
>Reading frame   0 time0.000   Segmentation fault
> 
> using a compiled version with "config --prefix 
> /home/cerezo/Programs/gromacs4.07" + "make" + "make install". However, it 
> works when I used a precompiled version (got with apt-get, I have kubuntu). 
> So I guess that it may be due to a mistake during the compilation. In 
> addition, other integrators (i.e. md, steep) work correctly with the version 
> I've compiled. My system is and Intel(R) Core(TM)2 Quad CPUQ8400  @ 
> 2.66GHz. Is there any trick I could try in the compilation?
> 
> I also tried gromacs-4.5-betaX and it works but sometimes (apparently 
> randomly) the calculation gets stops (as if it had entered in an infinite 
> loop) after reading the last frame.
> 
> Thanks for your attention!
> 
> Javier
> 
> -- 
> Javier CEREZO BASTIDA
> Estudiante de Doctorado
> -
> Dpto. Química-Física
> Universidad de Murcia
> 30100 MURCIA (España)
> Tlf.(+34)868887434
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface 
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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Re: [gmx-users] pdb2gmx-4.5 treats DNA as protein (and fails)

[David van der Spoel]

On 2010-08-16 12.34, Maiki wrote:

So, anybody knows why it does that or how to deal with nucleic acids?
I only saw one similar question asked recently (with different error)
which was also left without answer.

Not all force fields have complete support for DNA. Try Charmm.


Maiki wrote:

Hi,

I'm trying to convert protein-DNA complex using pdb2gmx with gromos53a6.ff

$ pdb2gmx -f del.pdb -o del.gro -p del.top -i del.itp -n del.ndx -ignh

In gromacs version 4.5-beta2 the result is:

Processing chain 3 'C' (516 atoms, 25 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Identified residue DT1 as a starting terminus.
Identified residue DA25 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'
Start terminus: NH3+
Warning: 'DA' not found in residue topology database, trying to use 'DADE'
End terminus: COO-
Warning: 'DT' not found in residue topology database, trying to use 'DTHY'
Warning: 'DA' not found in residue topology database, trying to use 'DADE'
Warning: 'DG' not found in residue topology database, trying to use 'DGUA'
(...)
Warning: 'DA' not found in residue topology database, trying to use 'DADE'

---
Program pdb2gmx, VERSION 4.5-beta2
Source code file: pdb2top.c, line: 922

Fatal error:
atom N not found in buiding block 1DT while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---







--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] pdb2gmx-4.5 treats DNA as protein (and fails)

[Maiki]

So, anybody knows why it does that or how to deal with nucleic acids?
I only saw one similar question asked recently (with different error)
which was also left without answer.

Maiki wrote:
> Hi,
>
> I'm trying to convert protein-DNA complex using pdb2gmx with gromos53a6.ff
>
> $ pdb2gmx -f del.pdb -o del.gro -p del.top -i del.itp -n del.ndx -ignh
>
> In gromacs version 4.5-beta2 the result is:
>
> Processing chain 3 'C' (516 atoms, 25 residues)
> There are 0 donors and 0 acceptors
> There are 0 hydrogen bonds
> Identified residue DT1 as a starting terminus.
> Identified residue DA25 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Warning: 'DT' not found in residue topology database, trying to use 'DTHY'
> Start terminus: NH3+
> Warning: 'DA' not found in residue topology database, trying to use 'DADE'
> End terminus: COO-
> Warning: 'DT' not found in residue topology database, trying to use 'DTHY'
> Warning: 'DA' not found in residue topology database, trying to use 'DADE'
> Warning: 'DG' not found in residue topology database, trying to use 'DGUA'
> (...)
> Warning: 'DA' not found in residue topology database, trying to use 'DADE'
>
> ---
> Program pdb2gmx, VERSION 4.5-beta2
> Source code file: pdb2top.c, line: 922
>
> Fatal error:
> atom N not found in buiding block 1DT while combining tdb and rtp
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
>   

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Re: [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells

[Anirban Ghosh]

Thanks a lot XAvier for clarifying my doubt. You mean to say "-rdd" option
with mdrun, right? And why does this curvature of the membrane occurs?

Thanks a lot once again.

Regards,

Anirban

On Mon, Aug 16, 2010 at 3:53 PM, XAvier Periole  wrote:

>
> Although a bit worrying the curvature of your bilayer is not
> responsible for the error message you are seeing.
>
> to solve the problem you have to increase to use the -rrd option
> (see manual for explanation). Typicaly a value of 1.4 to 1.6 should
> be fine.
>
>
> On Aug 16, 2010, at 12:16 PM, Anirban Ghosh wrote:
>
>  Hi ALL,
>>
>> I have made a CGMD system with multiple copies of a single protein in
>> bilayer, by replicating the monomer using genconf in the X-Y plane. After
>> running CGMD for about 100 ns, I am getting the following error:
>>
>>
>> 
>>   Energies (kJ/mol)
>>   Bond   G96AngleProper Dih.  Improper Dih.LJ (SR)
>>4.73694e+043.00928e+044.68451e+038.26028e+02   -1.29727e+06
>>   Coulomb (SR)  PotentialKinetic En.   Total EnergyTemperature
>>   -7.97216e+03   -1.7e+062.24656e+05   -9.97613e+053.21675e+02
>>  Pressure (bar)  Cons. rmsd ()
>>   -9.97540e+001.69233e-05
>>
>>
>> Not all bonded interactions have been properly assigned to the domain
>> decomposition cells
>>
>> A list of missing interactions:
>>G96Angle of  28064 missing  1
>>
>> Molecule type 'DSPC'
>> the first 10 missing interactions, except for exclusions:
>>G96Angle atoms   10   11   12  global  5309  5310  5311
>>
>> ---
>> Program mdrun_mpi, VERSION 4.0.7
>> Source code file: domdec_top.c, line: 341
>>
>> Fatal error:
>> 1 of the 62352 bonded interactions could not be calculated because some
>> atoms involved moved further apart than the multi-body cut-off distance (1.2
>> nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs
>> and tabulated bonds also see option -ddcheck
>>
>> 
>>
>> On visual inspection I found that the bilayer is becoming curved (image
>> attached). In the .top file I have mentioned the different monomers of my
>> system as:
>>
>>
>> --
>> [ system ]
>> PROT in DSPC Bilayer
>>
>> [ molecules ]
>> Protein 1
>> DSPC104
>> W   1397
>> NA+ 0
>> CL- 4
>> Protein 1
>> DSPC104
>> W   1397
>> NA+0
>> CL- 4
>>
>> -
>>
>> How can I resolve this error? Any suggestion is welcome.
>>
>> Regards,
>>
>> Anirban
>> --
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>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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Re: [gmx-users] Running MD on a dimeric protein

[XAvier Periole]

The way you define things would work fine but if
your dimer is an homodimer only one topology is
needed. topol_A and topolo_B should be identical.

The part of the mdp file is fine.

On Aug 16, 2010, at 7:13 AM, onetwo wrote:


Hello Sir,

I am simulating a protein which is a homodimer, when I did pdb2gmx,  
it generated a topolgy file in which there were two chain topologies  
for each chain as :


; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"

and in Compound section gave ;

Compound #mols
Protein_A 1
Protein_B 1

I want to ask that if it will consider the system as one or two  
different proteins.


Also in production MD phase, in md.mdp file I mentioned

Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300

I have this doubt that as I have given tc-grps as Protein and Non- 
Protein, so if "Protein" will consider both the chains of the  
protein or not.


Thanks in advance
Regards

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Re: [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells

[XAvier Periole]

Although a bit worrying the curvature of your bilayer is not
responsible for the error message you are seeing.

to solve the problem you have to increase to use the -rrd option
(see manual for explanation). Typicaly a value of 1.4 to 1.6 should
be fine.

On Aug 16, 2010, at 12:16 PM, Anirban Ghosh wrote:


Hi ALL,

I have made a CGMD system with multiple copies of a single protein  
in bilayer, by replicating the monomer using genconf in the X-Y  
plane. After running CGMD for about 100 ns, I am getting the  
following error:



   Energies (kJ/mol)
   Bond   G96AngleProper Dih.  Improper Dih. 
LJ (SR)
4.73694e+043.00928e+044.68451e+038.26028e+02
-1.29727e+06
   Coulomb (SR)  PotentialKinetic En.   Total Energy 
Temperature
   -7.97216e+03   -1.7e+062.24656e+05   -9.97613e+05 
3.21675e+02

 Pressure (bar)  Cons. rmsd ()
   -9.97540e+001.69233e-05


Not all bonded interactions have been properly assigned to the  
domain decomposition cells


A list of missing interactions:
G96Angle of  28064 missing  1

Molecule type 'DSPC'
the first 10 missing interactions, except for exclusions:
G96Angle atoms   10   11   12  global  5309  5310   
5311


---
Program mdrun_mpi, VERSION 4.0.7
Source code file: domdec_top.c, line: 341

Fatal error:
1 of the 62352 bonded interactions could not be calculated because  
some atoms involved moved further apart than the multi-body cut-off  
distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see  
option -rdd, for pairs and tabulated bonds also see option -ddcheck



On visual inspection I found that the bilayer is becoming curved  
(image attached). In the .top file I have mentioned the different  
monomers of my system as:


--
[ system ]
PROT in DSPC Bilayer

[ molecules ]
Protein 1
DSPC104
W   1397
NA+ 0
CL- 4
Protein 1
DSPC104
W   1397
NA+0
CL- 4
-

How can I resolve this error? Any suggestion is welcome.

Regards,

Anirban
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Re: [gmx-users] Running MD on a dimeric protein

[Justin A. Lemkul]

onetwo wrote:

Hello Sir,

I am simulating a protein which is a homodimer, when I did pdb2gmx, it 
generated a topolgy file in which there were two chain topologies for 
each chain as :


; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"

and in Compound section gave ;

Compound #mols
Protein_A 1
Protein_B 1

I want to ask that if it will consider the system as one or two 
different proteins.




Look in both topol_A.itp and topol_B.itp - you will find two separate molecules 
defined.



Also in production MD phase, in md.mdp file I mentioned

Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300

I have this doubt that as I have given tc-grps as Protein and 
Non-Protein, so if "Protein" will consider both the chains of the 
protein or not.




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

-Justin


Thanks in advance
Regards




--


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] Not all bonded interactions have been properly assigned to the domain decomposition cells

[Anirban Ghosh]

Hi ALL,

I have made a CGMD system with multiple copies of a single protein in
bilayer, by replicating the monomer using genconf in the X-Y plane. After
running CGMD for about 100 ns, I am getting the following error:


   Energies (kJ/mol)
   Bond   G96AngleProper Dih.  Improper Dih.LJ (SR)
4.73694e+043.00928e+044.68451e+038.26028e+02   -1.29727e+06
   Coulomb (SR)  PotentialKinetic En.   Total EnergyTemperature
   -7.97216e+03   -1.7e+062.24656e+05   -9.97613e+053.21675e+02
 Pressure (bar)  Cons. rmsd ()
   -9.97540e+001.69233e-05


Not all bonded interactions have been properly assigned to the domain
decomposition cells

A list of missing interactions:
G96Angle of  28064 missing  1

Molecule type 'DSPC'
the first 10 missing interactions, except for exclusions:
G96Angle atoms   10   11   12  global  5309  5310  5311

---
Program mdrun_mpi, VERSION 4.0.7
Source code file: domdec_top.c, line: 341

Fatal error:
1 of the 62352 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance (1.2
nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs
and tabulated bonds also see option -ddcheck


On visual inspection I found that the bilayer is becoming curved (image
attached). In the .top file I have mentioned the different monomers of my
system as:

--
[ system ]
PROT in DSPC Bilayer

[ molecules ]
Protein 1
DSPC104
W   1397
NA+ 0
CL- 4
Protein 1
DSPC104
W   1397
NA+0
CL- 4
-

How can I resolve this error? Any suggestion is welcome.

Regards,

Anirban
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RE: [gmx-users] tpi segmentation fault

[Berk Hess]

Hi,

I don't understand why 4.0.7 gives a segv.

But 4.5-beta probably gives a segv because of a parallel problem.
Could you try 4.5-beta with the mdrun option -nt 1
and report back?

Thanks,

Berk

> Date: Fri, 13 Aug 2010 18:35:55 +0200
> From: j...@um.es
> To: gmx-users@gromacs.org
> Subject: [gmx-users] tpi segmentation fault
> 
> Hi all.
> 
> I am trying to perform a tpi (test particle insertion) calculation on a 
> trajectory generated with mpi_mdrun (gromacs 4.0.7, run in a Beowulf 
> cluster of Intel(R) Core(TM)2 Quad CPUQ6600  @ 2.40GHz). I am using 
> tpi integrator in the mdp file and the following command:
> 
>   $  grompp -f tpi.mdp -c 32hoa_128dmpcwrun.gro -n index_tpi.ndx -p 
> topol_tpi.top
>   $  mdrun -rerun 32hoa_128dmpcwrun.trr -g tpi.log
> 
> I tried different versions of gromcas and for 4.0.X I got a segmentation 
> fault getting the message:
> 
>  trn version: GMX_trn_file (single precision)
>  Reading frame   0 time0.000   Segmentation fault
> 
> using a compiled version with "config --prefix 
> /home/cerezo/Programs/gromacs4.07" + "make" + "make install". However, 
> it works when I used a precompiled version (got with apt-get, I have 
> kubuntu). So I guess that it may be due to a mistake during the 
> compilation. In addition, other integrators (i.e. md, steep) work 
> correctly with the version I've compiled. My system is and Intel(R) 
> Core(TM)2 Quad CPUQ8400  @ 2.66GHz. Is there any trick I could try 
> in the compilation?
> 
> I also tried gromacs-4.5-betaX and it works but sometimes (apparently 
> randomly) the calculation gets stops (as if it had entered in an 
> infinite loop) after reading the last frame.
> 
> Thanks for your attention!
> 
> Javier
> 
> -- 
> Javier CEREZO BASTIDA
> Estudiante de Doctorado
> -
> Dpto. Química-Física
> Universidad de Murcia
> 30100 MURCIA (España)
> Tlf.(+34)868887434
> 
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[gmx-users] Running MD on a dimeric protein

[onetwo]

Hello Sir,

I am simulating a protein which is a homodimer, when I did pdb2gmx, it 
generated a topolgy file  in which there were two chain topologies for each 
chain as :  

; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"   

and in Compound section gave ;

Compound#mols
Protein_A   1
Protein_B   1

I want to ask that if it will consider the system as one or two different 
proteins.

Also in production MD phase, in md.mdp file I mentioned

Berendsen temperature coupling is on in two groups
Tcoupl  = V-rescale
tc-grps = Protein Non-Protein
tau_t   = 0.1 0.1
ref_t   = 300 300

I have this doubt that as I have given tc-grps as Protein and Non-Protein, so 
if "Protein" will consider both the chains of the protein or not.

Thanks in advance
Regards-- 
gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Parallel mdrun not working on gentoo linux

[Mark Abraham]

- Original Message -
From: Manik Mayur 
Date: Monday, August 16, 2010 3:02
Subject: Re: [gmx-users] Parallel mdrun not working on gentoo linux
To: Discussion list for GROMACS users 

> comments inline..
> 
> 2010/8/14 Mark Abraham :
> > Did you build a parallel GROMACS? If so, how? Do MPI test 
> programs run?
> 
> I used the following command..
> 
> ./configure --enable-mpi --disable-nice --with-fft=fftw3 --
> program-suffix=_mpi
> make mdrun
> make install-mdrun
> 
> and yes, mpi test programs are running fine.
> 
> further, $mdrun_mpi just results in a blinking cursor at newline
> (earlier it displayed an array of info strings)

That's weird. Sounds like a dynamic linking error. Is there another version of 
MPI installed? (Get rid of it.) Try enforcing static linking.

Or, try these http://gentoo-portage.com/sci-chemistry/gromacs

Mark

> > - Original Message -
> > From: Manik Mayur 
> > Date: Saturday, August 14, 2010 15:14
> > Subject: [gmx-users] Parallel mdrun not working on gentoo linux
> > To: Discussion list for GROMACS users 
> >
> >> Hi All,
> >>
> >> I am trying to build gromacs-4.0.7 on my gentoo box. My non-
> parallel>> version of mdrun is working without any issues but 
> when I try to run
> >> the parallel version of mdrun, it kind of hangs (even no help 
> info).>> Some details-
> >>
> >> 1) $uname -a
> >> Linux bingo 2.6.34-gentoo-r1 #7 SMP Fri Aug 13 10:18:23 IST 
> 2010 i686
> >> Intel(R) Core(TM)2 Quad CPU Q8200 @ 2.33GHz GenuineIntel GNU/Linux
> >>
> >> 2) openmpi -version : 1.4.1 (through emerge)
> >>
> >> 3) $ ldd /usr/local/bin/mdrun_mpi
> >> linux-gate.so.1 =>  (0xb77f6000)
> >> libmd_mpi.so.5 => /usr/local/gromacs/lib/libmd_mpi.so.5 
> (0xb76ee000)>> libgmx_mpi.so.5 => 
> /usr/local/gromacs/lib/libgmx_mpi.so.5>> (0xb746) 
> libxml2.so.2 => /usr/lib/libxml2.so.2 (0xb7321000)
> >> libz.so.1 => /lib/libz.so.1 (0xb730d000)
> >> libnsl.so.1 => /lib/libnsl.so.1 (0xb72f5000)
> >> libfftw3f.so.3 => /usr/lib/libfftw3f.so.3 (0xb71b2000)
> >> libm.so.6 => /lib/libm.so.6 (0xb718d000)
> >> libSM.so.6 => /usr/lib/libSM.so.6 (0xb7184000)
> >> libuuid.so.1 => /lib/libuuid.so.1 (0xb717f000)
> >> libICE.so.6 => /usr/lib/libICE.so.6 (0xb7166000)
> >> libX11.so.6 => /usr/lib/libX11.so.6 (0xb7041000)
> >> libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb7025000)
> >> libXau.so.6 => /usr/lib/libXau.so.6 (0xb7021000)
> >> libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0xb701b000)
> >> libdl.so.2 => /lib/libdl.so.2 (0xb7017000)
> >> libmpi.so.0 => /usr/lib/libmpi.so.0 (0xb6f84000)
> >> libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0xb6f3d000)
> >> libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0xb6ed2000)
> >> libutil.so.1 => /lib/libutil.so.1 (0xb6ece000)
> >> libpthread.so.0 => /lib/libpthread.so.0 (0xb6eb5000)
> >> libc.so.6 => /lib/libc.so.6 (0xb6d6f000)
> >> /lib/ld-linux.so.2 (0xb77f7000)
> >>
> >> Please somebody tell me what is the problem?
> >>
> >> Thanks,
> >>
> >> Manik Mayur
> >> --
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