[gmx-users] Entending water in negative Z direction

[chris . neale]

If you are using PBC, extending the positive direction *is* extending  
the negative direction, they are the same thing. If you really must  
center your bilayer on Z, then try editconf -translate 0 0 N


And please take this only as a useful suggestion, but simulating a  
GPCR in a membrane protein before fully understanding PBC is probably  
the wrong order to go about things. You might save yourself a heap of  
time in the end by starting with some simpler systems first.


Chris.

-- original message --

Hi ALL,

In previous posts I mentioned the problem I am facing: a portion of my  
protein (GPCR in a POPC bilayer) in extending out of the water box in  
negative Z-direction, how to extend the water in that direction. I  
have gone through the PBC section of the manual. While changing the Z  
coordinate value of the last line of the .gro file I am able to extend  
the water layer in the positive Z direction. But I am not able to  
extend it in the opposite direction. Decreasing the Z coordinate value  
is not helping that. How to do this? Any suggestion is welcome.


Regards,



 Anirban Ghosh

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Re: [gmx-users] Replacing the PRODRG charges

[Justin A. Lemkul]

Lucio Ricardo Montero Valenzuela wrote:

The target forcefield will be G43a1. But I would move to more recent
versions of GROMOS 53a5 or 53a6.


A more empirical charge assignment is often a reasonable starting point for 
assigning GROMOS charges.  As I understand it, quantum calculations were only 
done to get electron densities around each atom in various functional groups; 
the subsequent parameterization was done empirically.  You must then verify that 
the parameters match some condensed-phase criteria (the force field references 
will tell you what types).


I have gotten reasonable results based on assigning charges from comparable 
functional groups within the building blocks in, i.e. ffG53a6.rtp.


-Justin

El jue, 04-06-2009 a las 16:29 +1000, Mark Abraham escribió: 

Lucio Ricardo Montero Valenzuela wrote:

I want to run a MD in an unparameterized molecule similar to adenine. I can get
the approximated parameters in PRODRG. But I have read that PRODRG not always
give the correct charge. Is it a good idea to replace that charges using the
charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, GLYCAM and
OPLS forcefields)?. Or will it be mixing forcefields?.

That depends on your target forcefield for your MD.

Mark
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] gromacs website: "(There is currently no text in this page)"

[Mark Abraham]

pim schravendijk wrote:
Ah yes, but can't you configure an automatic server forward to do this? 
I can't imagine many people want to manually retype the url they get as 
a google result.


The transition period is presumably not going last very long, and I'd 
rather put up with some temporary losses in user convenience than have 
Erik(?) spending more of his time on this transition and less on doing 
science/GROMACS :-)


Google's going to have to have time to re-index the new website anyway..

Mark
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Re: [gmx-users] Entending water in negative Z direction

[Tsjerk Wassenaar]

Hi,

What is the difference between increasing in the positive z direction
and the negative z direction?

Tsjerk

On Thu, Jun 4, 2009 at 4:31 PM, Anirban Ghosh  wrote:
> Hi ALL,
>
> In previous posts I mentioned the problem I am facing: a portion of my
> protein (GPCR in a POPC bilayer) in extending out of the water box in
> negative Z-direction, how to extend the water in that direction. I have gone
> through the PBC section of the manual. While changing the Z coordinate value
> of the last line of the .gro file I am able to extend the water layer in the
> positive Z direction. But I am not able to extend it in the opposite
> direction. Decreasing the Z coordinate value is not helping that. How to do
> this? Any suggestion is welcome.
>
> Regards,
>
>
>
>
> Anirban Ghosh
> 
> Explore and discover exciting holidays and getaways with Yahoo! India Travel
> Click here!
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-- 
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Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
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Re: [gmx-users] Replacing the PRODRG charges

[Marc F. Lensink]

On Thu, Jun 04, 2009 at 03:46:59PM -0400, Justin A. Lemkul wrote:
>
>
> Lucio Ricardo Montero Valenzuela wrote:
>> The target forcefield will be G43a1. But I would move to more recent
>> versions of GROMOS 53a5 or 53a6.
>
> A more empirical charge assignment is often a reasonable starting point for 
> assigning GROMOS charges.  As I understand it, quantum calculations were 
> only done to get electron densities around each atom in various functional 
> groups; the subsequent parameterization was done empirically.  You must 
> then verify that the parameters match some condensed-phase criteria (the 
> force field references will tell you what types).
>
> I have gotten reasonable results based on assigning charges from comparable 
> functional groups within the building blocks in, i.e. ffG53a6.rtp.

I can second that.  charge transfer from comparable functional works
adequately for the gromos force field.  for opls/aa I've achieved
satisfactory results with resp charges.  I expect those will work well
for amber too.  compatibility between resp charges and the gromos
force field is not straightforward.

in any case, _any_ (new) parameterization needs to be verified and
validated!

cheers,
marc



-- 
Marc F. Lensink (Ph.D.)
Structure and Function of Biological MembranesSFMB
Centre for Structural Biology and Bioinformatics  CSBB
Université Libre de Bruxelles (ULB) marc.lens...@ulb.ac.be
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425
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[gmx-users] overrriding problem

[Rebeca García Fandiño]

Hi,
I am doing a simulation combining amber and Gaff force field (for dopc lipids), 
this is the first part of my topology file:

; UNK_GMX.top created by acpypi on Thu Jun  4 22:06:03 2009

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

[ atomtypes ]
;name   bond_type mass charge   ptype   sigma epsilon   Amb
 CA   CA  0.0  0.0   A 3.39967e-01   3.59824e-01 ; 1.91 
 0.0860
 CT   CT  0.0  0.0   A 3.39967e-01   4.57730e-01 ; 1.91 
 0.1094
 CC   0.0  0.0   A 3.39967e-01   3.59824e-01 ; 1.91 
 0.0860
 HO   HO  0.0  0.0   A 0.0e+00   0.0e+00 ; 0.00 
 0.
 OO   0.0  0.0   A 2.95992e-01   8.78640e-01 ; 1.66 
 0.2100
 OH   OH  0.0  0.0   A 3.06647e-01   8.80314e-01 ; 1.72 
 0.2104
 c3c3   12.0100-0.12654 A3.399676e-01
4.577296e-01 ; 1.91  0.1094
 hchc1.0080 0.02245 A2.649538e-01
6.568880e-02 ; 1.49  0.0157
 c2c2   12.0100-0.15458 A3.399676e-01
3.598240e-01 ; 1.91  0.0860
 haha1.0080 0.11146 A2.599647e-01
6.276000e-02 ; 1.46  0.0150
 c c12.0100 0.44800A3.399676e-01
3.598240e-01 ; 1.91  0.0860
 o o   16.-0.47180 A2.959927e-01
8.786400e-01 ; 1.66  0.2100
 osos   16.-0.15429 A3.18e-01
7.112800e-01 ; 1.68  0.1700
 h1h1 1.0080 0.16551A2.471358e-01
6.568880e-02 ; 1.39  0.0157
 p5p5  30.9700   1.14364A3.741781e-01
8.368000e-01 ; 2.10  0.2000
 n4n4   14.0100 0.01626 A3.250004e-01
7.112800e-01 ; 1.82  0.1700
 hxhx1.0080 0.08244 A1.959981e-01
6.568880e-02 ; 1.10  0.0157
 OWOW  0.0  0.0   A 3.16572e-01   6.49775e-01 ; 
1.78  0.1553
 HWHW  0.0  0.0   A 0.0e+00   0.0e+00 ; 
0.00  0.
 NaNa 0.0  0.0   A 2.15954e-01   1.47545e+00 ; 1.21 
 0.3526
 ClCl 0.0  0.0   A 4.83045e-01   5.34924e-02 ; 2.71 
 0.0128

When I try to minimize the system, with grompp -f minimizado.mdp -c 
final_system.gro -p final_system.top -o minimizado.tpr I find 2 warnings:

WARNING 1 [file final_system.top, line 19]:
  Overriding atomtype c
WARNING 2 [file final_system.top, line 20]:
  Overriding atomtype o

It is like it is not distinguing the capitals for amber and non-capitals for 
gaff. Does anybody know which can be the cause of these warnings?

Thank you very much,

Rebeca Garcia
University of Oxford

_
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[gmx-users] Re: goverrriding problem

[Alan]

Yep, contrary to AMBER, GMX is not case sensitive, so C and c are the same
and since you declare them twice you get this overriding warning.

However, I did acpypi aware of this (it should add '_' to e.g. c, making
'c_'). Unless you're doing something manually (as it seems). Otherwise it
would a pleasure to see this issue closely (can you send me your input
prmtop and inpcrd?).

Otherwise do it yourself by making c_ and o_ and the overriding warn will be
off.

Cheers,
Alan


>
> Message: 7
> Date: Thu, 4 Jun 2009 20:55:52 +
> From: Rebeca Garc?a Fandi?o 
> Subject: [gmx-users] overrriding problem
> To: 
> Message-ID: 
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi,
> I am doing a simulation combining amber and Gaff force field (for dopc
> lipids), this is the first part of my topology file:
>
> ; UNK_GMX.top created by acpypi on Thu Jun  4 22:06:03 2009
>
> [ defaults ]
> ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
> 1   2   yes 0.5 0.8333
>
> [ atomtypes ]
> ;name   bond_type mass charge   ptype   sigma epsilon
> Amb
>  CA   CA  0.0  0.0   A 3.39967e-01   3.59824e-01 ;
> 1.91  0.0860
>  CT   CT  0.0  0.0   A 3.39967e-01   4.57730e-01 ;
> 1.91  0.1094
>  CC   0.0  0.0   A 3.39967e-01   3.59824e-01 ;
> 1.91  0.0860
>  HO   HO  0.0  0.0   A 0.0e+00   0.0e+00 ;
> 0.00  0.
>  OO   0.0  0.0   A 2.95992e-01   8.78640e-01 ;
> 1.66  0.2100
>  OH   OH  0.0  0.0   A 3.06647e-01   8.80314e-01 ;
> 1.72  0.2104
>  c3c3   12.0100-0.12654 A3.399676e-01
>  4.577296e-01 ; 1.91  0.1094
>  hchc1.0080 0.02245 A2.649538e-01
>  6.568880e-02 ; 1.49  0.0157
>  c2c2   12.0100-0.15458 A3.399676e-01
>  3.598240e-01 ; 1.91  0.0860
>  haha1.0080 0.11146 A2.599647e-01
>  6.276000e-02 ; 1.46  0.0150
>  c c12.0100 0.44800A3.399676e-01
>  3.598240e-01 ; 1.91  0.0860
>  o o   16.-0.47180 A2.959927e-01
>  8.786400e-01 ; 1.66  0.2100
>  osos   16.-0.15429 A3.18e-01
>  7.112800e-01 ; 1.68  0.1700
>  h1h1 1.0080 0.16551A2.471358e-01
>  6.568880e-02 ; 1.39  0.0157
>  p5p5  30.9700   1.14364A3.741781e-01
>  8.368000e-01 ; 2.10  0.2000
>  n4n4   14.0100 0.01626 A3.250004e-01
>  7.112800e-01 ; 1.82  0.1700
>  hxhx1.0080 0.08244 A1.959981e-01
>  6.568880e-02 ; 1.10  0.0157
>  OWOW  0.0  0.0   A 3.16572e-01   6.49775e-01 ;
> 1.78  0.1553
>  HWHW  0.0  0.0   A 0.0e+00   0.0e+00 ;
> 0.00  0.
>  NaNa 0.0  0.0   A 2.15954e-01   1.47545e+00 ;
> 1.21  0.3526
>  ClCl 0.0  0.0   A 4.83045e-01   5.34924e-02 ;
> 2.71  0.0128
>
> When I try to minimize the system, with grompp -f minimizado.mdp -c
> final_system.gro -p final_system.top -o minimizado.tpr I find 2 warnings:
>
> WARNING 1 [file final_system.top, line 19]:
>  Overriding atomtype c
> WARNING 2 [file final_system.top, line 20]:
>  Overriding atomtype o
>
> It is like it is not distinguing the capitals for amber and non-capitals
> for gaff. Does anybody know which can be the cause of these warnings?
>
> Thank you very much,
>
> Rebeca Garcia
> University of Oxford
>

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

[krishnakumar]

Hi,

Has any one encountered this error while using g_hbond?

*

Select a group: 12
Selected 12: 'SOL'
Select a group: 12
Selected 12: 'SOL'
Calculating hydrogen bonds in SOL (20949 atoms)

---
Program g_hbond, VERSION 4.0.4
Source code file: gmx_hbond.c, line: 565

Fatal error:
Error in func_type Position Rest.
---



I get this error only when using trajectory with positional restraint during
MD.
Is there any fix for this bug?

Thanks
Krishna
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Re: [gmx-users] g_hbond error

[Justin A. Lemkul]

krishnakumar wrote:

Hi,

Has any one encountered this error while using g_hbond?

*

Select a group: 12
Selected 12: 'SOL'
Select a group: 12
Selected 12: 'SOL'
Calculating hydrogen bonds in SOL (20949 atoms)

---
Program g_hbond, VERSION 4.0.4
Source code file: gmx_hbond.c, line: 565

Fatal error:
Error in func_type Position Rest.
---



I get this error only when using trajectory with positional restraint 
during MD.

Is there any fix for this bug?



Probably not, unless you submit a bugzilla :)  The search page is not working 
properly due to the website migration, so it might be hard to determine if 
anyone else has reported such a problem.  It may be due to the fact that typical 
use of position restraints is for equilibration, with the PR time period getting 
discarded (not analyzed).  Thus, you are doing an analysis that was unforeseen.


If you want to analyze this portion of the trajectory, you could create a new 
.tpr file (identical to your original, but without defining position restraints 
in the .mdp file), and trying to run the analysis again.  If that alleviates the 
problem, it would be useful to include as part of a bugzilla report.


-Justin


Thanks
Krishna




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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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: goverrriding problem

[Rebeca García Fandiño]

Thank you very much, Alan.

In this case, I am not using acpypi, since I am using a topology for dopc 
already published, and it is already converted into Gromacs. So, it´s  
manually, as you suppose. I will follow your suggestion and change c and o by 
c_ and o_.

Best wishes,

Rebeca.
 


From: alanwil...@gmail.com
Date: Thu, 4 Jun 2009 22:19:30 +0100
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: goverrriding problem



Yep, contrary to AMBER, GMX is not case sensitive, so C and c are the same and 
since you declare them twice you get this overriding warning.


However, I did acpypi aware of this (it should add '_' to e.g. c, making 'c_'). 
Unless you're doing something manually (as it seems). Otherwise it would a 
pleasure to see this issue closely (can you send me your input prmtop and 
inpcrd?).


Otherwise do it yourself by making c_ and o_ and the overriding warn will be 
off.


Cheers,
Alan
 

Message: 7
Date: Thu, 4 Jun 2009 20:55:52 +
From: Rebeca Garc?a Fandi?o 
Subject: [gmx-users] overrriding problem
To: 
Message-ID: 
Content-Type: text/plain; charset="iso-8859-1"


Hi,
I am doing a simulation combining amber and Gaff force field (for dopc lipids), 
this is the first part of my topology file:

; UNK_GMX.top created by acpypi on Thu Jun  4 22:06:03 2009

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

[ atomtypes ]
;name   bond_type mass charge   ptype   sigma epsilon   Amb
 CA   CA  0.0  0.0   A 3.39967e-01   3.59824e-01 ; 1.91 
 0.0860
 CT   CT  0.0  0.0   A 3.39967e-01   4.57730e-01 ; 1.91 
 0.1094
 CC   0.0  0.0   A 3.39967e-01   3.59824e-01 ; 1.91 
 0.0860
 HO   HO  0.0  0.0   A 0.0e+00   0.0e+00 ; 0.00 
 0.
 OO   0.0  0.0   A 2.95992e-01   8.78640e-01 ; 1.66 
 0.2100
 OH   OH  0.0  0.0   A 3.06647e-01   8.80314e-01 ; 1.72 
 0.2104
 c3c3   12.0100-0.12654 A3.399676e-01
4.577296e-01 ; 1.91  0.1094
 hchc1.0080 0.02245 A2.649538e-01
6.568880e-02 ; 1.49  0.0157
 c2c2   12.0100-0.15458 A3.399676e-01
3.598240e-01 ; 1.91  0.0860
 haha1.0080 0.11146 A2.599647e-01
6.276000e-02 ; 1.46  0.0150
 c c12.0100 0.44800A3.399676e-01
3.598240e-01 ; 1.91  0.0860
 o o   16.-0.47180 A2.959927e-01
8.786400e-01 ; 1.66  0.2100
 osos   16.-0.15429 A3.18e-01
7.112800e-01 ; 1.68  0.1700
 h1h1 1.0080 0.16551A2.471358e-01
6.568880e-02 ; 1.39  0.0157
 p5p5  30.9700   1.14364A3.741781e-01
8.368000e-01 ; 2.10  0.2000
 n4n4   14.0100 0.01626 A3.250004e-01
7.112800e-01 ; 1.82  0.1700
 hxhx1.0080 0.08244 A1.959981e-01
6.568880e-02 ; 1.10  0.0157
 OWOW  0.0  0.0   A 3.16572e-01   6.49775e-01 ; 
1.78  0.1553
 HWHW  0.0  0.0   A 0.0e+00   0.0e+00 ; 
0.00  0.
 NaNa 0.0  0.0   A 2.15954e-01   1.47545e+00 ; 1.21 
 0.3526
 ClCl 0.0  0.0   A 4.83045e-01   5.34924e-02 ; 2.71 
 0.0128

When I try to minimize the system, with grompp -f minimizado.mdp -c 
final_system.gro -p final_system.top -o minimizado.tpr I find 2 warnings:

WARNING 1 [file final_system.top, line 19]:
 Overriding atomtype c
WARNING 2 [file final_system.top, line 20]:
 Overriding atomtype o

It is like it is not distinguing the capitals for amber and non-capitals for 
gaff. Does anybody know which can be the cause of these warnings?

Thank you very much,

Rebeca Garcia
University of Oxford

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<

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Re: [gmx-users] Scaled 1-5 interactions

[Mark Abraham]

Borys Szefczyk wrote:

Dear GROMACS Users,

I would like to use the OPLS force field, but with additional scaling
factor for the Coulomb 1-5 interactions for certain atoms. More precisely,
I want to use the standard 0.5 scaling for Coulomb and LJ 1-4 interactions
and 0.8 scaling factor for Coulomb 1-5 interactions. Is there a way to
do this within the topology file of Gromacs or do I need to modify the code?


I can't think of a way to do this natively. Trying to use fudge-LJ for 
1-4 and pairs for 1-5 won't work (see 5.7.1 of manual).


Setting the number of exclusions for a moleculetype to 4, in a 
forcefield with "generate_pairs = yes" and "fudgeLJ = 0.5" will probably 
see pdb2gmx get everything except the 1-5 interactions right. Then you 
post-process the .top from pdb2gmx in a (e.g.) perl script, using the [ 
bonds ] entries to recognize 1-5 interactions (which you add as [ pairs 
]). You look up the normal LJ functions for those atom types, then 
invoking the combination rule and your 0.8 scaling and write parameters 
on the [ pairs ] entry for each 1-5 pair. grompp will then blindly eat 
what you give it. Such 1-5 interactions will be reported by mdrun in 
with the normal LJ interactions.


Mark
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[gmx-users] reference group in constant velocity pulling, GMX 4

[Simba Xiao]

Dear all,

I am using the pulling code in gromacs 4.0.5 with constant velocity pulling.

My case is pulling protein in two opposite directions, which I do not want
any other extra force acting on the protein.

So I did not assign any reference group in the simulation, and I got a
warning saying that:  absolut coordinates is used as reference group and it
will cause artifacts.

According to the manual, ( 0, 0, 0 ) is used as reference group, but I still
do not understand what kind of artifacts could happen.

The only thing I can think of is the periodical boundary, but I am not sure,
could any one have any idea?

Thanks!

-- 
Senbo Xiao

PICB, Shanghai, 200031
CHINA
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[gmx-users] Re: Extending water in negative Z direction

[Anirban Ghosh]

Hi ALL,

Thanks for the reply. I think what I mean will be more clear by just having a 
look at the structure (attached). I have tried by increasing the Z value, as 
suggested by David, but that only extends the water on one side of the bilayer 
only and not on the other side (which I need). Please have a look at the 
structure.
Thanks a lot.

Regards,


 Anirban GhoshGrade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India



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Re: [gmx-users] Re: Extending water in negative Z direction

[David van der Spoel]

Anirban Ghosh wrote:

Hi ALL,

Thanks for the reply. I think what I mean will be more clear by just 
having a look at the structure (attached). I have tried by increasing 
the Z value, as suggested by David, but that only extends the water on 
one side of the bilayer only and not on the other side (which I need). 
Please have a look at the structure.

Thanks a lot.


Please go back to the manual and read about PBC.





Regards,


 
*Anirban Ghosh*

*Grade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India
*



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--
David.

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se

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Re: [gmx-users] Re: Extending water in negative Z direction

[Tsjerk Wassenaar]

Anirban,

Please, many of us have years of experience with MD and this type of
systems. If you had considered that, rather than assuming that we
still don't understand what you mean, you would have been on the right
track to fix an apparent caveat in your knowledge regarding MD
simulations, and notably periodic boundary conditions. Your system is
periodic. That means that one side of your box is equal to the other
side. You have an infinite system, or a wrapped system. In the
coordinate file you maybe see something that can be represented as:

|P--|

Where P is your protein, the dashes represent the water layer and the
vertical bars represent the box edges. But under PBC that means you
have

|P--||P--||P--||P--| etc

Now you can't see the box edges in such a system, so it's exactly like having

P--P--P--P--

And that means you have water on both sides of the protein. You can
shift the system a bit and take one part out:

|---P---|

It's exactly the same thing! There just isn't another side in a periodic system.

As Justin pointed out, this is one of the very basic aspects of MD
simulations. It is vital to understand it before starting simulations,
and you should not try and go for expert topics like simulations of
GPCRs in membranes before mastering the basics.

I hope this makes things clear.

Cheers,

Tsjerk

On Fri, Jun 5, 2009 at 8:25 AM, Anirban Ghosh wrote:
> Hi ALL,
>
> Thanks for the reply. I think what I mean will be more clear by just having
> a look at the structure (attached). I have tried by increasing the Z value,
> as suggested by David, but that only extends the water on one side of the
> bilayer only and not on the other side (which I need). Please have a look at
> the structure.
> Thanks a lot.
>
> Regards,
>
>
>
> Anirban Ghosh
> Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
>
> 
> Bollywood news, movie reviews, film trailers and more! Click here.
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] how to include ionic strength

[Mark Abraham]

amri ta wrote:

Dear gromacs users,
 
I am simulating a protein which works in salt solution within cell. I 
have to include 4M salt (say, NaCl) to the simulation box. How can i 
include such ionic strength? Please outline me the procedure.


If you do some tutorial material, you will find out the procedure for 
adding ions. Finding out how many ions to add is for you to calculate :-)


Mark
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[gmx-users] DSSP problem

[rituraj purohit]

Dear all
I want ti install DSSP for visualization of secondary structure in
gromacs analysis.
I am doing following procedure..
Copy the executable "dsspcmbi"  to /usr/bin or /usr/local/bin
  ln -s dsspcmbi dssp
And running it for my Pdb like that
dssp file.pdb file.dssp

BUt I am getting error "Permission Denied" even i m super user for the
machine (root).

[r...@localhost ~]# dssp
bash: /usr/local/bin/dssp: Permission denied
[r...@localhost ~]#

Plaese any body tell the solution for this problem...

Regard
Rituraj



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Re: [gmx-users] DSSP problem

[Mark Abraham]

rituraj purohit wrote:

Dear all
I want ti install DSSP for visualization of secondary structure in
gromacs analysis.
I am doing following procedure..
Copy the executable "dsspcmbi"  to /usr/bin or /usr/local/bin
  ln -s dsspcmbi dssp
And running it for my Pdb like that
dssp file.pdb file.dssp

BUt I am getting error "Permission Denied" even i m super user for the
machine (root).

[r...@localhost ~]# dssp
bash: /usr/local/bin/dssp: Permission denied
[r...@localhost ~]#

Plaese any body tell the solution for this problem...


You may still need execute permissions on the original executable. You 
should not ever be running as root when not installing software or 
maintaining the system.


Mark
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[gmx-users] DSSP problem

[rituraj purohit]

PMF calculation
>  To: gmx-users@gromacs.org
>  Message-ID: <20090604135651.2wdhcqo28csw8...@webmail1.sjtu.edu.cn>
>  Content-Type: text/plain;   charset=GB2312; DelSp="Yes";
> format="flowed"
>
>  Dear All:
>
>   I want to do some PMF (Potenial of Mean Force) calculation by
>  AFM pulling method using the pull code to study the unbinding of a
>  protein and a ligand.
>
>   I want pull the ligand from its binding site and calculate the
>  PMF of the procedure, does it possible?
>
>   I have read the user manual about PMF calculation carefully, but
>  still not clear how to do . Does anyone have any tutorial about how to
>  do this kind of calculation or any published papers doing this things?
>  anyhelp is greatly appreciate!
>
>
> Best Wishes
>  R-X Gu
>
>
>
>  --
>
>  Message: 3
>  Date: Thu, 04 Jun 2009 01:24:32 -0500
>  From: Lucio Ricardo Montero Valenzuela 
>  Subject: [gmx-users] Replacing the PRODRG charges
>  To: gmx-users@gromacs.org
>  Message-ID: <1244096672.4a2768a0e4...@webmail.ibt.unam.mx>
>  Content-Type: text/plain; charset=ISO-8859-1
>
>  I want to run a MD in an unparameterized molecule similar to adenine. I can 
> get
>  the approximated parameters in PRODRG. But I have read that PRODRG not always
>  give the correct charge. Is it a good idea to replace that charges using the
>  charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, GLYCAM 
> and
>  OPLS forcefields)?. Or will it be mixing forcefields?.
>
>  Lucio Ricardo Montero Valenzuela
>  Instituto de Biotecnologia, UNAM
>  Departamento de Biologia Molecular de Plantas
>  Av. Universidad 2001, Col. Chamilpa
>  Cuernavaca 62210
>  Mexico
>
>  
>  Este mensaje fue enviado desde el servidor Webmail del Instituto de 
> Biotecnologia.
>
>
>  --
>
>  Message: 4
>  Date: Thu, 04 Jun 2009 16:29:03 +1000
>  From: Mark Abraham 
>  Subject: Re: [gmx-users] Replacing the PRODRG charges
>  To: Discussion list for GROMACS users 
>  Message-ID: <4a2769af.6000...@anu.edu.au>
>  Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>  Lucio Ricardo Montero Valenzuela wrote:
>  > I want to run a MD in an unparameterized molecule similar to adenine. I 
> can get
>  > the approximated parameters in PRODRG. But I have read that PRODRG not 
> always
>  > give the correct charge. Is it a good idea to replace that charges using 
> the
>  > charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, GLYCAM 
> and
>  > OPLS forcefields)?. Or will it be mixing forcefields?.
>
>  That depends on your target forcefield for your MD.
>
>  Mark
>
>
>  --
>
>  Message: 5
>  Date: Thu, 4 Jun 2009 12:27:00 +0530 (IST)
>  From: amri ta 
>  Subject: [gmx-users] how to include ionic strength
>  To: gmx-users@gromacs.org
>  Message-ID: <418624.33836...@web8708.mail.in.yahoo.com>
>  Content-Type: text/plain; charset="iso-8859-1"
>
>  Dear gromacs users,
>
>  I am simulating a protein which works in salt solution within cell. I have 
> to include 4M salt (say, NaCl) to the simulation box. How can i include such 
> ionic strength? Please outline me the procedure.
>
>  Thanks in advance.
>  Amrita Paul
>
>
>
>
>   Cricket on your mind? Visit the ultimate cricket website. Enter 
> http://beta.cricket.yahoo.com
>  -- next part --
>  An HTML attachment was scrubbed...
>  URL: 
> http://www.gromacs.org/pipermail/gmx-users/attachments/20090604/84086c55/attachment-0001.html
>
>  --
>
>  Message: 6
>  Date: Thu, 04 Jun 2009 17:09:35 +1000
>  From: Mark Abraham 
>  Subject: Re: [gmx-users] how to include ionic strength
>  To: Discussion list for GROMACS users 
>  Message-ID: <4a27732f.1020...@anu.edu.au>
>  Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>  amri ta wrote:
>  > Dear gromacs users,
>  >
>  > I am simulating a protein which works in salt solution within cell. I
>  > have to include 4M salt (say, NaCl) to the simulation box. How can i
>  > include such ionic strength? Please outline me the procedure.
>
>  If you do some tutorial material, you will find out the procedure for
>  adding ions. Finding out how many ions to add is for you to calculate :-)
>
>  Mark
>
>
>  --
>
>  Message: 7
>  Date: Thu, 4 Jun 2009 12:52:32 +0530
>  From: ri

[gmx-users] gromos type in .rtp file

[subarna thakur]

hello everyone
Can any body please explain to me, what does the trm gb_38 or gb_39 stand for 
under the bond coulmn of the .rtp file ? what is gromos type under angles and 
impropers?

Subarna 


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Re: [gmx-users] gromos type in .rtp file

[XAvier Periole]

On Jun 4, 2009, at 10:10 AM, subarna thakur wrote:


hello everyone
Can any body please explain to me, what does the trm gb_38 or gb_39  
stand for under the bond coulmn of the ..rtp file ? what is gromos  
type under angles and impropers?
gb_XX stands for the XX type of gromos bond, ga_XX for the XX gromos  
angle type, gd_XX for the dihedral and so on.
you'll find their definition in the file ffGYYYbon.itp file, where YYY  
can be G43a1, G53a6 ...


Subarna

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Re: [gmx-users] DSSP problem

[Manik Mayur]

h).
> >
> >  My BG/L FFTW-3.2 configure line is
> >
> >  ../configure --prefix /hpc/home/mja163/progs CC=blrts_xlc --host=powerpc
> >  --build=ppc64 CFLAGS=-qbgl -qarch=440d -qtune=440 -qnoautoconfig -O5
> >  --disable-fortran --enable-float
> >
> >  but you may need to tweak that for BG/P for all I know. Let me know
> >  when/if something works and I'll update the wiki.
> >
> >  Mark
> >
> >
> >  --
> >
> >  Message: 2
> >  Date: Thu, 04 Jun 2009 13:56:51 +0800
> >  From: mirc...@sjtu.edu.cn
> >  Subject: [gmx-users] about PMF calculation
> >  To: gmx-users@gromacs.org
> >  Message-ID: <20090604135651.2wdhcqo28csw8...@webmail1.sjtu.edu.cn>
> >  Content-Type: text/plain;   charset=GB2312; DelSp="Yes";
>  format="flowed"
> >
> >  Dear All:
> >
> >   I want to do some PMF (Potenial of Mean Force) calculation by
> >  AFM pulling method using the pull code to study the unbinding of a
> >  protein and a ligand.
> >
> >   I want pull the ligand from its binding site and calculate the
> >  PMF of the procedure, does it possible?
> >
> >   I have read the user manual about PMF calculation carefully, but
> >  still not clear how to do . Does anyone have any tutorial about how to
> >  do this kind of calculation or any published papers doing this things?
> >  anyhelp is greatly appreciate!
> >
> >
> > Best Wishes
> >  R-X Gu
> >
> >
> >
> >  --
> >
> >  Message: 3
> >  Date: Thu, 04 Jun 2009 01:24:32 -0500
> >  From: Lucio Ricardo Montero Valenzuela 
> >  Subject: [gmx-users] Replacing the PRODRG charges
> >  To: gmx-users@gromacs.org
> >  Message-ID: <1244096672.4a2768a0e4...@webmail.ibt.unam.mx>
> >  Content-Type: text/plain; charset=ISO-8859-1
> >
> >  I want to run a MD in an unparameterized molecule similar to adenine. I
> can get
> >  the approximated parameters in PRODRG. But I have read that PRODRG not
> always
> >  give the correct charge. Is it a good idea to replace that charges using
> the
> >  charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER,
> GLYCAM and
> >  OPLS forcefields)?. Or will it be mixing forcefields?.
> >
> >  Lucio Ricardo Montero Valenzuela
> >  Instituto de Biotecnologia, UNAM
> >  Departamento de Biologia Molecular de Plantas
> >  Av. Universidad 2001, Col. Chamilpa
> >  Cuernavaca 62210
> >  Mexico
> >
> >  
> >  Este mensaje fue enviado desde el servidor Webmail del Instituto de
> Biotecnologia.
> >
> >
> >  --
> >
> >  Message: 4
> >  Date: Thu, 04 Jun 2009 16:29:03 +1000
> >  From: Mark Abraham 
> >  Subject: Re: [gmx-users] Replacing the PRODRG charges
> >  To: Discussion list for GROMACS users 
> >  Message-ID: <4a2769af.6000...@anu.edu.au>
> >  Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >  Lucio Ricardo Montero Valenzuela wrote:
> >  > I want to run a MD in an unparameterized molecule similar to adenine.
> I can get
> >  > the approximated parameters in PRODRG. But I have read that PRODRG not
> always
> >  > give the correct charge. Is it a good idea to replace that charges
> using the
> >  > charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER,
> GLYCAM and
> >  > OPLS forcefields)?. Or will it be mixing forcefields?.
> >
> >  That depends on your target forcefield for your MD.
> >
> >  Mark
> >
> >
> >  --
> >
> >  Message: 5
> >  Date: Thu, 4 Jun 2009 12:27:00 +0530 (IST)
> >  From: amri ta 
> >  Subject: [gmx-users] how to include ionic strength
> >  To: gmx-users@gromacs.org
> >  Message-ID: <418624.33836...@web8708.mail.in.yahoo.com>
> >  Content-Type: text/plain; charset="iso-8859-1"
> >
> >  Dear gromacs users,
> >
> >  I am simulating a protein which works in salt solution within cell. I
> have to include 4M salt (say, NaCl) to the simulation box. How can i include
> such ionic strength? Please outline me the procedure.
> >
> >  Thanks in advance.
> >  Amrita Paul
> >
> >
> >
> >
> >   Cricket on your mind? Visit the ultimate cricket website. Enter
> http://beta.cricket.yahoo.com
> >  

[gmx-users] gromacs website: "(There is currently no text in this page)"

[pim schravendijk]

Hi,

there seems to be a discrepancy between google results from the gromacs
pages and the pages themselves.
If going to results on the mailing list or for example:

www.*gromacs*.org/documentation/howtos/*mpich*_howto.html

I see the gromacs page, and the submenu seems to be ok, but the page is
empty except for:

(There is currently no text in this page)

This might be quite inconvenient, as information from google results is only
available via the google cache at the moment.


-- 
Greetings, Pim
http://www.molmod.com
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Re: [gmx-users] gromacs website: "(There is currently no text in this page)"

[Justin A. Lemkul]

pim schravendijk wrote:

Hi,

there seems to be a discrepancy between google results from the gromacs 
pages and the pages themselves.

If going to results on the mailing list or for example:

www.*gromacs*.org/documentation/howtos/*mpich*_howto.html

I see the gromacs page, and the submenu seems to be ok, but the page is 
empty except for:


(There is currently no text in this page)

This might be quite inconvenient, as information from google results is 
only available via the google cache at the moment.




As explained on the homepage, the site is undergoing some changes.  You can 
access all the old content at oldwww.gromacs.org, so the page you want is 
available at:


oldwww.gromacs.org/documentation/howtos/mpich_howto.html

-Justin



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http://www.molmod.com




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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] gromacs website: "(There is currently no text in this page)"

[pim schravendijk]

Ah yes, but can't you configure an automatic server forward to do this? I
can't imagine many people want to manually retype the url they get as a
google result.

On Thu, Jun 4, 2009 at 2:23 PM, Justin A. Lemkul  wrote:

>
>
> pim schravendijk wrote:
>
>> Hi,
>>
>> there seems to be a discrepancy between google results from the gromacs
>> pages and the pages themselves.
>> If going to results on the mailing list or for example:
>>
>> www.*gromacs*.org/documentation/howtos/*mpich*_howto.html
>>
>> I see the gromacs page, and the submenu seems to be ok, but the page is
>> empty except for:
>>
>> (There is currently no text in this page)
>>
>> This might be quite inconvenient, as information from google results is
>> only available via the google cache at the moment.
>>
>>
> As explained on the homepage, the site is undergoing some changes.  You can
> access all the old content at oldwww.gromacs.org, so the page you want is
> available at:
>
> oldwww.gromacs.org/documentation/howtos/mpich_howto.html
>
> -Justin
>
>
>> --
>> Greetings, Pim
>> http://www.molmod.com
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
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>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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http://www.molmod.com
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Re: [gmx-users] DSSP problem

[Mark Abraham]

rituraj purohit wrote:

Dear mark
Where i can get the file with permission.
I downloaded from   http://swift.cmbi.kun.nl/gv/dssp/


Please do not send copies of entire digests in your emails. That breaks 
searches and wastes time and bandwidth.


You give the file permissions in the standard Unix way with chmod. 
Please try to search for your own solutions first - 5 seconds with 
Google should result in this page: 
http://en.wikipedia.org/wiki/File_system_permissions


Mark
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Re: [gmx-users] Replacing the PRODRG charges

[Lucio Ricardo Montero Valenzuela]

The target forcefield will be G43a1. But I would move to more recent
versions of GROMOS 53a5 or 53a6.
El jue, 04-06-2009 a las 16:29 +1000, Mark Abraham escribió: 
> Lucio Ricardo Montero Valenzuela wrote:
> > I want to run a MD in an unparameterized molecule similar to adenine. I can 
> > get
> > the approximated parameters in PRODRG. But I have read that PRODRG not 
> > always
> > give the correct charge. Is it a good idea to replace that charges using the
> > charges given with the R.E.D.vIII using ESP-A1 (suitable for AMBER, GLYCAM 
> > and
> > OPLS forcefields)?. Or will it be mixing forcefields?.
> 
> That depends on your target forcefield for your MD.
> 
> Mark
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[gmx-users] Scaled 1-5 interactions

[Borys Szefczyk]

Dear GROMACS Users,

I would like to use the OPLS force field, but with additional scaling
factor for the Coulomb 1-5 interactions for certain atoms. More precisely,
I want to use the standard 0.5 scaling for Coulomb and LJ 1-4 interactions
and 0.8 scaling factor for Coulomb 1-5 interactions. Is there a way to
do this within the topology file of Gromacs or do I need to modify the code?

Regards,
Borys Szefczyk

-- 
 REQUIMTE,  &  Molecular Modelling & Quantum Chemistry Group,
  Department of Chemistry,  &  Institute of Physical & Theoretical Chemistry,
   Faculty of Science,  &  Wroclaw University of Technology
   University of Porto  &  http://ichfit.ch.pwr.wroc.pl/people/szefczyk
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[gmx-users] Entending water in negative Z direction

[Anirban Ghosh]

Hi ALL,

In previous posts I mentioned the problem I am facing: a portion of my protein 
(GPCR in a POPC bilayer) in extending out of the water box in negative 
Z-direction, how to extend the water in that direction. I have gone through the 
PBC section of the manual. While changing the Z coordinate value of the last 
line of the .gro file I am able to extend the water layer in the positive Z 
direction. But I am not able to extend it in the opposite direction. Decreasing 
the Z coordinate value is not helping that. How to do this? Any suggestion is 
welcome.

Regards,



 Anirban Ghosh


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Re: [gmx-users] Entending water in negative Z direction

[David van der Spoel]

Anirban Ghosh wrote:

Hi ALL,

In previous posts I mentioned the problem I am facing: a portion of my 
protein (GPCR in a POPC bilayer) in extending out of the water box in 
negative Z-direction, how to extend the water in that direction. I have 
gone through the PBC section of the manual. While changing the Z 
coordinate value of the last line of the .gro file I am able to extend 
the water layer in the positive Z direction. But I am not able to extend 
it in the opposite direction. Decreasing the Z coordinate value is not 
helping that. How to do this? Any suggestion is welcome.



Increase the z-coordinate.


Regards,



 
*Anirban Ghosh*




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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
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[gmx-users] diffusion coefficient with g_msd

[Sarah Witzke]

Dear gromacs users,

 

I have done several simulations with small lipophilic, molecules diffusing into 
a DMPC bilayer.

I would like to calculate the diffusion coefficient of the molecules inside the 
membrane, and therefore I looked at g_msd. The manual (version 4.0) states on 
p. 250 (manual pages) that g_msd uses the Einstein relation. Reading "Molecular 
Modelling: principles and applications" 2.ed. by Andrew Leach it is explained 
that the "for calculating the diffusion coefficient the mean-squared distances 
should not be limited by the edges of the periodic box. In other words, we 
require a set of positions that have not been translated back into the central 
simulation cell." This makes sense since I try to calculate the distance a 
molecule diffuse.

I haven't been able to find any mention of how gromacs handle this either in 
the manual or on the wiki page. The search function on the old webpage directs 
me to the new webpage, which doesn't give any results for "g_msd" or "diffusion 
coefficient" or alike, so my apologies for asking a question I could have found 
the answer to I old emails. When I google I get some of the old emails on g_msd 
from the gromacs website, but I can only read some of them (the others direct 
me to an empty page in the new webpage). 

 

The first question is whether I can use my .xtc file made with this command 
from the original .trr file:

trjconv -f dmpclim32-all.trr -novel -center -fit rot+trans -pbc whole -s 
dmpclim32-1.tpr -o dmpclim32-all.xtc  (for fitting and centring the DMPC group 
is used)

I would guess I could not, but should I then do the command again creating a 
new .xtc file, but without using -center and -pbc whole?

 

My second question is why g_msd has the option -rmcomm to remove COM motion? 
How is g_msd created so that the diffusion coefficient can be calculated if COM 
motion is removed?

 

Thank you very much for your time,

Sarah

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