[gmx-users] Water-Mediated Hydrogen Bonds

[Raja Pandian]

Dear All,



I’m doing research in the field of Protein-DNA interaction. I have gone
through these papers,

*A “Solvated Rotamer” Approach to Modeling Water-Mediated Hydrogen Bonds at
Protein–Protein Interfaces*

*“Effect on DNA relaxation of the single Thr718Ala mutation in human
topoisomerase I: a functional and molecular dynamics study”*

*“Molecular Dynamics Simulation Study of Interaction between Model Rough
Hydrophobic Surfaces.”*

*“Prediction of Protein Binding to DNA in the Presence of Water-Mediated
Hydrogen Bonds”*



I have found lot of interesting things on these papers that will be useful
for the progress of my research carrier.

I have been looking for water mediated hydrogen bond in my simulation when i
use g_hbond the -ins option it dose not showing the water mediated hydrogen
bond could you please tell me how to get the hydrogen mediated hydrogen bond
and water mediated free energy in Gromacs ?

Is there any way to calculate water mediated hydrogen bond between
Protein-DNA using Gromacs tools?

If it is possible, please send your program (water mediated hydrogen bond
derivation program) to me and also the program operating procedure.



Eagerly waiting for your reply.

Thanking You



Faithfully

Raja
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] N-terminus problem

[Mark Abraham]

On 1/07/2011 8:35 PM, Emine Deniz Tekin wrote:


Hi Gromacs users,


I created a lipopeptide (lauroic acid connected to an 8-residue 
peptide which starts with Valine).




How is the link from acid to peptide created?

·If I try to use pdb2gmx with -ter flag(Start terminus VAL-2: None, 
End terminus ASP-9: COO-), everything seems to work (topology is 
created.).




Does that topology work for MD? Why does pdb2gmx think there's 9 
residues, and below there seem to be 63?


·But, if I try to use pdb2gmx with -ter flagfor more than one 
lipopeptide at desired positions, it gives the following error. (again 
says Start terminus VAL-2: None, End terminus ASP-9: COO- )


*Fatal error:  Atom N not found in residue seq.nr . 1 
while adding improper*


While I was creating the lipopeptide, I introduced the lauroic acid as 
a pseudo amino acid (following Mark’s suggestion). So, I really do NOT 
have atom N in the first residue. I pasted a part of my gro file below.




Some improper in your topology database entries wants a N atom that 
doesn't exist. Unfortunately, we don't have anywhere near enough 
information to guess why. pdb2gmx is trying to match your .rtp and 
specbond entries to your .gro file, but only seeing the latter can't 
help diagnose a mismatch. Some description of "desired positions" is 
also important.


Also, giving full command lines are always preferred. You may not think 
anything significant is there, and you might be right, but if there 
*can* be something significant there, and we aren't given the chance to 
know whether it is present, we might just not bother to waste time 
guessing :)


Mark



GROMACS molecule input test

574

1DPPCA111.0275.2953.153

1DPPCB210.8945.2993.078

1DPPCG310.7775.2343.153

1DPPCD410.6455.2543.078

1DPPCE510.5215.2033.153

1DPPCZ610.3925.2513.086

1DPPCM710.2665.2073.161

1DPPCN810.1405.2723.103

1DPPCO910.0145.2213.172

1DPPCP109.8855.2793.112

1DPPCQ119.7615.2033.160

1DPPC1211.1015.4303.147

1DPPO1311.0325.5313.136

2VALN1411.2355.4503.160

2VALH1511.2495.5503.159

2VALCA1611.3685.3853.181

2VALCB1711.3905.2333.181

2VALCG11811.3325.1723.308

2VALCG21911.3385.1613.056

2VALC2011.4865.4493.103

2VALO2111.4985.4362.982

..

63ASPOD1570-0.30614.8743.343

63ASPOD2571-0.45115.0303.289

63ASPC572-0.05715.0233.106

63ASPO15730.01415.0033.207

63ASPO2574-0.02915.1043.017

16.2393716.2393716.23937


I am using Gromacs 53a6 force field and gromacs 4.5.3 version.

Any help will be appreciated.

Thanks in advance

Deniz



-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] energygrps long-range interaction

[Justin A. Lemkul]

Please make sure to keep the discussion on the gmx-users list.

gyorgy.han...@fc.up.pt wrote:


Thank you very much for the reply.
So I guess the same holds for all Ewald-like long-corrections, right?


Sounds right.


But we don't have this problem with reaction field correction do we?



Presumably, since the effect of the reaction field is uniform beyond rcoulomb. 
The problem with RF is the discontinuity present at the cutoff.


-Justin


Gyorgy


Citando "Justin A. Lemkul" :




gyorgy.han...@fc.up.pt wrote:


Dear Users,

I'm wondering if it is possible to extract the long-range part of  
the interactions of energy-groups. In the output I see only  
short-range terms.


I am interested in the total interaction energy of an energy group. 
 I would guess that one should be able to get the long-range part of  
the interactions somehow... Or am I wrong?




In the case of PME, there is no simple solution.  This has been
discussed a number of times in the list archive.  Some potential
solutions have been presented about how one might potentially separate
group contributions, but the usefulness of this information is
debatable.

-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists







--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] how is dVpot/dlambda calculated

[Justin A. Lemkul]

Dennis Sprous, PhD wrote:
Could someone forward the citation of how dVpot/dlambda is calculated 
for a free energy run.


I am specifically interested in knowing if it is an analytic or numeric 
based calculation.




The equations relevant to free energy calculations are discussed in the manual, 
section 4.5.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] how is dVpot/dlambda calculated

[Dennis Sprous, PhD]

Could someone forward the citation of how dVpot/dlambda is calculated 
for a free energy run.


I am specifically interested in knowing if it is an analytic or numeric 
based calculation.


--
any problemworth attack
proves its worth   by fighting back

Dennis Sprous, PhD
BioLeap Inc.
Cambridge MA 02141

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] interaction energy

[Justin A. Lemkul]

balaji nagarajan wrote:

Dear users !

thanks for the reply

I was able to do that , otherwise we can select the number of the option 
one by one  and enter then after that if we leave a  empty line and


enter  it gives all the needed energy terms !


my intension is not to do like this

is it possible to give it along the

g_energy

like

 g_energy -f  em.edr --- ( any options can be given along with this  ,

i tried
g_energy -f  em.edr 11 0 ( it is not working )

how it can be done ?



http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive

-Justin



 


 > Date: Fri, 1 Jul 2011 13:53:59 -0400
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] interaction energy
 >
 >
 >
 > balaji nagarajan wrote:
 > >
 > >
 > >
 > > Dear Users !
 > >
 > > i would like to do this to a set of files !
 > > so how to print the required values in the text mode or is there any
 > > flag for this in
 >
 > I quoted the help description for how to do this. Is there some 
problem? For
 > instance, if you want to write the potential energy to an .xvg file, 
type:

 >
 > 11 0
 >
 > and hit Enter. The values will be printed.
 >
 > -Justin
 >
 > > g_energy ,
 > >
 > > thanks in advance
 > >
 > >
 > > > Date: Fri, 1 Jul 2011 13:40:28 -0400
 > > > From: jalem...@vt.edu
 > > > To: gmx-users@gromacs.org
 > > > Subject: Re: [gmx-users] interaction energy
 > > >
 > > >
 > > >
 > > > balaji nagarajan wrote:
 > > > > Dear Users !
 > > > >
 > > > > Now i am able to do the protein solvent interaction !
 > > > >
 > > > > thanks ! i have understood !
 > > > >
 > > > > when i used the energygrps ,
 > > > > when i used the
 > > > > g_energy -f em.edr
 > > > >
 > > > > this command it prints all terms and asks to make selection as 
below,

 > > > >
 > > > > 1 Bond 2 Angle 3 Proper-Dih. 4
 > > > > Ryckaert-Bell.
 > > > > 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 LJ-(LR)
 > > > > 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Pressure
 > > > > 13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
 > > > > 17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
 > > > > 21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
 > > > > 25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
 > > > > 29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
 > > > > 33 Mu-Y 34 Mu-Z
 > > > > 35 Coul-SR:Protein-Protein 36 LJ-SR:Protein-Protein
 > > > > 37 LJ-LR:Protein-Protein 38 Coul-14:Protein-Protein
 > > > > 39 LJ-14:Protein-Protein 40 Coul-SR:Protein-SOL
 > > > > 41 LJ-SR:Protein-SOL 42 LJ-LR:Protein-SOL
 > > > > 43 Coul-14:Protein-SOL 44 LJ-14:Protein-SOL
 > > > > 45 Coul-SR:SOL-SOL 46 LJ-SR:SOL-SOL
 > > > > 47 LJ-LR:SOL-SOL 48 Coul-14:SOL-SOL
 > > > > 49 LJ-14:SOL-SOL 50 T-rest
 > > > >
 > > > > ---
 > > > >
 > > > > how one can write this all to a file !
 > > > >
 > > >
 > > > As prompted by g_energy:
 > > >
 > > > "Select the terms you want from the following list by
 > > > selecting either (part of) the name or the number or a combination.
 > > > End your selection with an empty line or a zero."
 > > >
 > > > Writing all terms to the same output file will result in nothing 
but an

 > > > incoherent mess. Choose terms wisely based on what you actually need
 > > to analyze.
 > > >
 > > > -Justin
 > > >
 > > > --
 > > > 
 > > >
 > > > Justin A. Lemkul
 > > > Ph.D. Candidate
 > > > ICTAS Doctoral Scholar
 > > > MILES-IGERT Trainee
 > > > Department of Biochemistry
 > > > Virginia Tech
 > > > Blacksburg, VA
 > > > jalemkul[at]vt.edu | (540) 231-9080
 > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 > > >
 > > > 
 > > > --
 > > > gmx-users mailing list gmx-users@gromacs.org
 > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > > > Please search the archive at
 > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 > > > Please don't post (un)subscribe requests to the list. Use the
 > > > www interface or send it to gmx-users-requ...@gromacs.org.
 > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 > >
 >
 > --
 > 
 >
 > Justin A. Lemkul
 > Ph.D. Candidate
 > ICTAS Doctoral Scholar
 > MILES-IGERT Trainee
 > Department of Biochemistry
 > Virginia Tech
 > Blacksburg, VA
 > jalemkul[at]vt.edu | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
 > 
 > --
 > gmx-users mailing list gmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send it to gmx-users-requ...@gromacs.org.
 > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of 

RE: [gmx-users] interaction energy

[balaji nagarajan]

Dear users ! 

thanks for the reply 

I was able to do that , otherwise we can select the number of the option one by 
one  and enter then after that if we leave a  empty line and 

enter  it gives all the needed energy terms ! 


my intension is not to do like this 

is it possible to give it along the 

g_energy 

like 

 g_energy -f  em.edr --- ( any options can be given along with this  , 

i tried 
g_energy -f  em.edr 11 0 ( it is not working ) 

how it can be done ? 


  

> Date: Fri, 1 Jul 2011 13:53:59 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] interaction energy
> 
> 
> 
> balaji nagarajan wrote:
> > 
> > 
> > 
> > Dear Users !
> > 
> > i would like to do this to a set of files !
> > so how to print the required values in the text mode or is there any 
> > flag for this in
> 
> I quoted the help description for how to do this.  Is there some problem?  
> For 
> instance, if you want to write the potential energy to an .xvg file, type:
> 
> 11 0
> 
> and hit Enter.  The values will be printed.
> 
> -Justin
> 
> > g_energy ,
> > 
> > thanks in advance
> > 
> > 
> >  > Date: Fri, 1 Jul 2011 13:40:28 -0400
> >  > From: jalem...@vt.edu
> >  > To: gmx-users@gromacs.org
> >  > Subject: Re: [gmx-users] interaction energy
> >  >
> >  >
> >  >
> >  > balaji nagarajan wrote:
> >  > > Dear Users !
> >  > >
> >  > > Now i am able to do the protein solvent interaction !
> >  > >
> >  > > thanks ! i have understood !
> >  > >
> >  > > when i used the energygrps ,
> >  > > when i used the
> >  > > g_energy -f em.edr
> >  > >
> >  > > this command it prints all terms and asks to make selection as below,
> >  > >
> >  > > 1 Bond 2 Angle 3 Proper-Dih. 4
> >  > > Ryckaert-Bell.
> >  > > 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 LJ-(LR)
> >  > > 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Pressure
> >  > > 13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
> >  > > 17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
> >  > > 21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
> >  > > 25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
> >  > > 29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
> >  > > 33 Mu-Y 34 Mu-Z
> >  > > 35 Coul-SR:Protein-Protein 36 LJ-SR:Protein-Protein
> >  > > 37 LJ-LR:Protein-Protein 38 Coul-14:Protein-Protein
> >  > > 39 LJ-14:Protein-Protein 40 Coul-SR:Protein-SOL
> >  > > 41 LJ-SR:Protein-SOL 42 LJ-LR:Protein-SOL
> >  > > 43 Coul-14:Protein-SOL 44 LJ-14:Protein-SOL
> >  > > 45 Coul-SR:SOL-SOL 46 LJ-SR:SOL-SOL
> >  > > 47 LJ-LR:SOL-SOL 48 Coul-14:SOL-SOL
> >  > > 49 LJ-14:SOL-SOL 50 T-rest
> >  > >
> >  > > ---
> >  > >
> >  > > how one can write this all to a file !
> >  > >
> >  >
> >  > As prompted by g_energy:
> >  >
> >  > "Select the terms you want from the following list by
> >  > selecting either (part of) the name or the number or a combination.
> >  > End your selection with an empty line or a zero."
> >  >
> >  > Writing all terms to the same output file will result in nothing but an
> >  > incoherent mess. Choose terms wisely based on what you actually need 
> > to analyze.
> >  >
> >  > -Justin
> >  >
> >  > --
> >  > 
> >  >
> >  > Justin A. Lemkul
> >  > Ph.D. Candidate
> >  > ICTAS Doctoral Scholar
> >  > MILES-IGERT Trainee
> >  > Department of Biochemistry
> >  > Virginia Tech
> >  > Blacksburg, VA
> >  > jalemkul[at]vt.edu | (540) 231-9080
> >  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >  >
> >  > 
> >  > --
> >  > gmx-users mailing list gmx-users@gromacs.org
> >  > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >  > Please search the archive at 
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >  > Please don't post (un)subscribe requests to the list. Use the
> >  > www interface or send it to gmx-users-requ...@gromacs.org.
> >  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
  -- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subsc

Re: [gmx-users] interaction energy

[Justin A. Lemkul]

balaji nagarajan wrote:




Dear Users !

i would like to do this to a set of files !
so how to print the required values in the text mode or is there any 
flag for this in


I quoted the help description for how to do this.  Is there some problem?  For 
instance, if you want to write the potential energy to an .xvg file, type:


11 0

and hit Enter.  The values will be printed.

-Justin


g_energy ,

thanks in advance


 > Date: Fri, 1 Jul 2011 13:40:28 -0400
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] interaction energy
 >
 >
 >
 > balaji nagarajan wrote:
 > > Dear Users !
 > >
 > > Now i am able to do the protein solvent interaction !
 > >
 > > thanks ! i have understood !
 > >
 > > when i used the energygrps ,
 > > when i used the
 > > g_energy -f em.edr
 > >
 > > this command it prints all terms and asks to make selection as below,
 > >
 > > 1 Bond 2 Angle 3 Proper-Dih. 4
 > > Ryckaert-Bell.
 > > 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 LJ-(LR)
 > > 9 Coulomb-(SR) 10 Coul.-recip. 11 Potential 12 Pressure
 > > 13 Vir-XX 14 Vir-XY 15 Vir-XZ 16 Vir-YX
 > > 17 Vir-YY 18 Vir-YZ 19 Vir-ZX 20 Vir-ZY
 > > 21 Vir-ZZ 22 Pres-XX 23 Pres-XY 24 Pres-XZ
 > > 25 Pres-YX 26 Pres-YY 27 Pres-YZ 28 Pres-ZX
 > > 29 Pres-ZY 30 Pres-ZZ 31 #Surf*SurfTen 32 Mu-X
 > > 33 Mu-Y 34 Mu-Z
 > > 35 Coul-SR:Protein-Protein 36 LJ-SR:Protein-Protein
 > > 37 LJ-LR:Protein-Protein 38 Coul-14:Protein-Protein
 > > 39 LJ-14:Protein-Protein 40 Coul-SR:Protein-SOL
 > > 41 LJ-SR:Protein-SOL 42 LJ-LR:Protein-SOL
 > > 43 Coul-14:Protein-SOL 44 LJ-14:Protein-SOL
 > > 45 Coul-SR:SOL-SOL 46 LJ-SR:SOL-SOL
 > > 47 LJ-LR:SOL-SOL 48 Coul-14:SOL-SOL
 > > 49 LJ-14:SOL-SOL 50 T-rest
 > >
 > > ---
 > >
 > > how one can write this all to a file !
 > >
 >
 > As prompted by g_energy:
 >
 > "Select the terms you want from the following list by
 > selecting either (part of) the name or the number or a combination.
 > End your selection with an empty line or a zero."
 >
 > Writing all terms to the same output file will result in nothing but an
 > incoherent mess. Choose terms wisely based on what you actually need 
to analyze.

 >
 > -Justin
 >
 > --
 > 
 >
 > Justin A. Lemkul
 > Ph.D. Candidate
 > ICTAS Doctoral Scholar
 > MILES-IGERT Trainee
 > Department of Biochemistry
 > Virginia Tech
 > Blacksburg, VA
 > jalemkul[at]vt.edu | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
 > 
 > --
 > gmx-users mailing list gmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send it to gmx-users-requ...@gromacs.org.
 > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

RE: [gmx-users] interaction energy

[balaji nagarajan]

Dear Users ! 

i would like to do this to a set of files ! 
so how to print the required values in the text mode or is there any flag for 
this in 
g_energy , 

thanks in advance 


> Date: Fri, 1 Jul 2011 13:40:28 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] interaction energy
> 
> 
> 
> balaji nagarajan wrote:
> > Dear Users !
> > 
> > Now i am able to do the protein solvent interaction !
> > 
> > thanks ! i have understood !
> > 
> > when i used the energygrps  ,
> > when i used the
> > g_energy -f em.edr
> > 
> > this command it prints all terms and asks to make selection as below,
> > 
> >  1  Bond 2  Angle3  Proper-Dih.  4  
> > Ryckaert-Bell.
> >   5  LJ-146  Coulomb-14   7  LJ-(SR)  8  LJ-(LR)
> >   9  Coulomb-(SR)10  Coul.-recip.11  Potential   12  Pressure
> >  13  Vir-XX  14  Vir-XY  15  Vir-XZ  16  Vir-YX
> >  17  Vir-YY  18  Vir-YZ  19  Vir-ZX  20  Vir-ZY
> >  21  Vir-ZZ  22  Pres-XX 23  Pres-XY 24  Pres-XZ
> >  25  Pres-YX 26  Pres-YY 27  Pres-YZ 28  Pres-ZX
> >  29  Pres-ZY 30  Pres-ZZ 31  #Surf*SurfTen   32  Mu-X
> >  33  Mu-Y34  Mu-Z
> >  35  Coul-SR:Protein-Protein 36  LJ-SR:Protein-Protein
> >  37  LJ-LR:Protein-Protein   38  Coul-14:Protein-Protein
> >  39  LJ-14:Protein-Protein   40  Coul-SR:Protein-SOL
> >  41  LJ-SR:Protein-SOL   42  LJ-LR:Protein-SOL
> >  43  Coul-14:Protein-SOL 44  LJ-14:Protein-SOL
> >  45  Coul-SR:SOL-SOL 46  LJ-SR:SOL-SOL
> >  47  LJ-LR:SOL-SOL   48  Coul-14:SOL-SOL
> >  49  LJ-14:SOL-SOL   50  T-rest
> > 
> > ---
> > 
> > how one can write this all to a file !
> > 
> 
> As prompted by g_energy:
> 
> "Select the terms you want from the following list by
> selecting either (part of) the name or the number or a combination.
> End your selection with an empty line or a zero."
> 
> Writing all terms to the same output file will result in nothing but an 
> incoherent mess.  Choose terms wisely based on what you actually need to 
> analyze.
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
  -- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] interaction energy

[Justin A. Lemkul]

balaji nagarajan wrote:

Dear Users !

Now i am able to do the protein solvent interaction !

thanks ! i have understood !

when i used the energygrps  ,
when i used the
g_energy -f em.edr

this command it prints all terms and asks to make selection as below,

 1  Bond 2  Angle3  Proper-Dih.  4  
Ryckaert-Bell.

  5  LJ-146  Coulomb-14   7  LJ-(SR)  8  LJ-(LR)
  9  Coulomb-(SR)10  Coul.-recip.11  Potential   12  Pressure
 13  Vir-XX  14  Vir-XY  15  Vir-XZ  16  Vir-YX
 17  Vir-YY  18  Vir-YZ  19  Vir-ZX  20  Vir-ZY
 21  Vir-ZZ  22  Pres-XX 23  Pres-XY 24  Pres-XZ
 25  Pres-YX 26  Pres-YY 27  Pres-YZ 28  Pres-ZX
 29  Pres-ZY 30  Pres-ZZ 31  #Surf*SurfTen   32  Mu-X
 33  Mu-Y34  Mu-Z
 35  Coul-SR:Protein-Protein 36  LJ-SR:Protein-Protein
 37  LJ-LR:Protein-Protein   38  Coul-14:Protein-Protein
 39  LJ-14:Protein-Protein   40  Coul-SR:Protein-SOL
 41  LJ-SR:Protein-SOL   42  LJ-LR:Protein-SOL
 43  Coul-14:Protein-SOL 44  LJ-14:Protein-SOL
 45  Coul-SR:SOL-SOL 46  LJ-SR:SOL-SOL
 47  LJ-LR:SOL-SOL   48  Coul-14:SOL-SOL
 49  LJ-14:SOL-SOL   50  T-rest

---

how one can write this all to a file !



As prompted by g_energy:

"Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero."

Writing all terms to the same output file will result in nothing but an 
incoherent mess.  Choose terms wisely based on what you actually need to analyze.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] interaction energy

[balaji nagarajan]

Dear Users ! 

Now i am able to do the protein solvent interaction ! 

thanks ! i have understood !

when i used the energygrps  , 
when i used the 
g_energy -f em.edr

this command it prints all terms and asks to make selection as below, 

 1  Bond 2  Angle3  Proper-Dih.  4  Ryckaert-Bell.
  5  LJ-146  Coulomb-14   7  LJ-(SR)  8  LJ-(LR)
  9  Coulomb-(SR)10  Coul.-recip.11  Potential   12  Pressure
 13  Vir-XX  14  Vir-XY  15  Vir-XZ  16  Vir-YX
 17  Vir-YY  18  Vir-YZ  19  Vir-ZX  20  Vir-ZY
 21  Vir-ZZ  22  Pres-XX 23  Pres-XY 24  Pres-XZ
 25  Pres-YX 26  Pres-YY 27  Pres-YZ 28  Pres-ZX
 29  Pres-ZY 30  Pres-ZZ 31  #Surf*SurfTen   32  Mu-X
 33  Mu-Y34  Mu-Z
 35  Coul-SR:Protein-Protein 36  LJ-SR:Protein-Protein
 37  LJ-LR:Protein-Protein   38  Coul-14:Protein-Protein
 39  LJ-14:Protein-Protein   40  Coul-SR:Protein-SOL
 41  LJ-SR:Protein-SOL   42  LJ-LR:Protein-SOL
 43  Coul-14:Protein-SOL 44  LJ-14:Protein-SOL
 45  Coul-SR:SOL-SOL 46  LJ-SR:SOL-SOL
 47  LJ-LR:SOL-SOL   48  Coul-14:SOL-SOL
 49  LJ-14:SOL-SOL   50  T-rest

---

how one can write this all to a file ! 

thanks in advance ! 



  -- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] energygrps long-range interaction

[Justin A. Lemkul]

gyorgy.han...@fc.up.pt wrote:


Dear Users,

I'm wondering if it is possible to extract the long-range part of the 
interactions of energy-groups. In the output I see only short-range terms.


I am interested in the total interaction energy of an energy group. I 
would guess that one should be able to get the long-range part of the 
interactions somehow... Or am I wrong?




In the case of PME, there is no simple solution.  This has been discussed a 
number of times in the list archive.  Some potential solutions have been 
presented about how one might potentially separate group contributions, but the 
usefulness of this information is debatable.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] energygrps long-range interaction

[gyorgy . hantal]

Dear Users,

I'm wondering if it is possible to extract the long-range part of the  
interactions of energy-groups. In the output I see only short-range  
terms.


I am interested in the total interaction energy of an energy group. I  
would guess that one should be able to get the long-range part of the  
interactions somehow... Or am I wrong?


Thanks in advance.

Gyorgy

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] micelle clustering

[Tsjerk Wassenaar]

Hi Sulatha,

With my clustering algorithm there can be no infinite loop :)
By the way, sorry for the error messages you ran into with compiling
4.0.7. It had escaped me that these changes were made after that
version.

Cheers,

Tsjerk

On Fri, Jul 1, 2011 at 8:29 AM, sulatha M. S  wrote:
> Thanks Mark,
> I will do the analysis in 4.5.4. Hope while doing the micelle clustering I
> will not get into a infinite loop as in 4.0.7.
> If I understand correctly, While using trjconv -pbc cluster,  I should use
> -e 0.002  or the frames (-dump option) in the xtc file  (generated after the
> micelles are formed)
>
> Sulatha
>
>
> 2011/7/1 Mark Abraham 
>>
>> On 1/07/2011 3:35 PM, sulatha M. S wrote:
>>>
>>> Hi Tsjerk,
>>>
>>> I installed gromacs myself. I put the modified gmx_trjconv.c code in the
>>> /src/tools subdirectory where the source code is located and tried the
>>> command
>>> make trjconv
>>> But it gives me a series of error messages, as given below.
>>
>> They're all mismatches because of changes between 4.0.7 and 4.5.4
>>
>>> My gromacs version is 4.0.7. I would like to continue in this version
>>> till I finish the set of runs which I have been doing before moving into
>>> 4.5.4 version. or else can I do the analysis alone in gromacs 4.5.4 with the
>>> xtc files generated from 4.0.7 version?
>>
>> Do that. The file formats are unchanged.
>>
>> Mark
>>
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] solvent_protein interaction energy

[Justin A. Lemkul]

balaji nagarajan wrote:


Thanks for the reply !

I have tried building the topology with  generating the index file

make_ndx  -f  * 


it gave options i have selected the protein and the solvent



An index file is unnecessary for default groups.

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


then i gave minimization

in the minimization file i have included

energygrps = Protein SOL ,


but the energy file have the same when i removed and inserted the above 
flag !


if any one can explain me in detail it will be helpfull



EM is a poor choice for testing; not all options designed to work with MD 
integrators are incorporated in simple EM procedures, although I do not see why 
(in this case) it shouldn't work.  A better test is a zero-step MD run (md 
integrator).  Note that not all terms are decomposable pairwise, just 
short-range nonbonded terms.


-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] 3rd neighbor

[Justin A. Lemkul]

Otto Master wrote:

Hi Everyone,
I would like to do some changes to the non bonded parameter of GROMOS 
force field. Especially, I like modify the 3rd neighbor parameters. 
Unfortunately, I cannot find them in the ffnonbonded.itp file. I assume 
that the parameter in [ atomtypes ] block are taken from Table 7 
(Oostenbring et al. JCC 2004, 53A6) and the [ nonbond_params ] contain 
the hard coded parameter of Table 8. So, where are the parameter of 
table 9 written?




These are in [pairtypes].  See manual section 5.3.4.

-Justin

--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] solvent_protein interaction energy

[balaji nagarajan]

Thanks for the reply ! 

I have tried building the topology with  generating the index file 

make_ndx  -f  *  

it gave options i have selected the protein and the solvent 

then i gave minimization 

in the minimization file i have included 

energygrps = Protein SOL , 


but the energy file have the same when i removed and inserted the above flag ! 

if any one can explain me in detail it will be helpfull 

thanks in advance ! 
  -- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_velacc

[Nilesh Dhumal]

Hello,

I am trying to calculate the velocity autocorrelation function for my
system. I have a system with glucose + ionic liquids (128 emi (cations)
and 128 Cl (anions)).

I am not getting proper velocity autocorrelation function.

 g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize  -e 10 -o


Attached the velocity autocorrelation function.


I am using Gromacs 4.0.7 version.


Thanks

Nilesh









vac.pdf
Description: Adobe PDF document
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] N-terminus problem

[Emine Deniz Tekin]

Hi Gromacs users,


I created a lipopeptide (lauroic acid  connected to an 8-residue peptide
which starts with Valine).

· If I try to use pdb2gmx with -ter flag   (Start terminus VAL-2:
None, End terminus ASP-9: COO-), everything seems to work (topology is
created.).

· But, if I try to use pdb2gmx with -ter flag  for more than one
lipopeptide at desired positions, it gives the following error. (again says
Start terminus VAL-2: None, End terminus ASP-9: COO- )

 *Fatal error:  Atom N not found in residue seq.nr. 1 while adding improper*

While I was creating the lipopeptide, I introduced the lauroic acid as a
pseudo amino acid (following Mark’s suggestion). So, I really do NOT have
atom N in the first residue. I pasted a part of my gro file below.


GROMACS molecule input test

574

1DPP CA1  11.027   5.295   3.153

1DPP CB2  10.894   5.299   3.078

1DPP CG3  10.777   5.234   3.153

1DPP CD4  10.645   5.254   3.078

1DPP CE5  10.521   5.203   3.153

1DPP CZ6  10.392   5.251   3.086

1DPP CM7  10.266   5.207   3.161

1DPP CN8  10.140   5.272   3.103

1DPP CO9  10.014   5.221   3.172

1DPP CP   10   9.885   5.279   3.112

1DPP CQ   11   9.761   5.203   3.160

1DPP  C   12  11.101   5.430   3.147

1DPP  O   13  11.032   5.531   3.136

2VAL  N   14  11.235   5.450   3.160

2VAL  H   15  11.249   5.550   3.159

2VAL CA   16  11.368   5.385   3.181

2VAL CB   17  11.390   5.233   3.181

2VALCG1   18  11.332   5.172   3.308

2VALCG2   19  11.338   5.161   3.056

2VAL  C   20  11.486   5.449   3.103

2VAL  O   21  11.498   5.436   2.982

..

   63ASPOD1  570  -0.306  14.874   3.343

   63ASPOD2  571  -0.451  15.030   3.289

   63ASP  C  572  -0.057  15.023   3.106

   63ASP O1  573   0.014  15.003   3.207

   63ASP O2  574  -0.029  15.104   3.017

  16.23937   16.23937   16.23937


I am using Gromacs 53a6 force field and gromacs 4.5.3 version.

Any help will be appreciated.

 Thanks in advance



Deniz
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Installation of gromacs-gpu on windows

[Андрей Гончар]

Thank you for your reply! Now can I have your attention for another
quetsion? I'm not very experienced in Visual Studio because I do
almost all of my work under linux. But now it is necessary to compile
gromacs-gpu under windows. Could someone point me to a tutorial or
how-to about step-by-step compiling of gpu-accelerated gromacs under
windows, because now i'm totally confused... Thanks in advance!

2011/6/30 Szilárd Páll :
> Dear Andrew,
>
> Compiling on Windows was tested only using MSVC and I have no idea if
> it works or not under cygwin. You should just try, both cmake and gcc
> is available for cygwin so you might be lucky and get mdrun-gpu
> compiled without any additional effort.
>
> All binaries on the Gromacs webpage _are outdated_ which is clearly
> stated on the respective page.
>
> Cheers,
> --
> Szilárd
>
>
>
> On Fri, Jun 24, 2011 at 9:54 AM, Андрей Гончар  wrote:
>> Hello! I have a misunderstood about the installation of gpu-enabled
>> gromacs under windows.
>> I'll try to explain: in system requirements of gromacs-gpu it is wrote
>> that Nvidia CUDA libraries have to be installed. But is it possible to
>> do under cygwin? This quertion appears because we run gromacs under
>> windows and so under cygwin.
>> Is there a way to compile gromacs-gpu on cygwin? Will the binaries
>> from gromacs-gpu page work and if so which of them to prefer to run
>> under cygwin? Those for windows or for linux?
>>
>> --
>>
>> Andrew Gontchar
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 

Андрей Гончар
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] 3rd neighbor

[Otto Master]

Hi Everyone,
I would like to do some changes to the non bonded parameter of GROMOS force
field. Especially, I like modify the 3rd neighbor parameters. Unfortunately,
I cannot find them in the ffnonbonded.itp file. I assume that the parameter
in [ atomtypes ] block are taken from Table 7 (Oostenbring et al. JCC 2004,
53A6) and the [ nonbond_params ] contain the hard coded parameter of Table
8. So, where are the parameter of table 9 written?

Thanks in advance
Otto
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] PME energy calculation

[Mark Abraham]

On 1/07/2011 5:51 PM, 李浩 wrote:
>
> Hello Everyone,
>
> I am using PME(4.05) to calculate the long-rang electrostatic
> interaction, but when I finished the
>
> Simulation, I found that I can’t get the result of energy of the part
> of “fourier space（long range part）”. In other word，there is only a
> congregation of energy of that named Coul. recip. Is there any way
> that I can get the energy of “group to group” of the “fourier space” ?
>

There are many threads on this topic in the archives. Basically, the
nature of that part of the calculation means that there's no convenient
way to do this, even if the result would mean anything.

Mark
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Energy-groups?

[Jianguo Li]

You can specify the energygrps in mdp file, grompp a new tpr file and use 
-rerun 
option of the mdrun to get a new edr file

Cheers
Jianguo 







From: "nishap.pa...@utoronto.ca" 
To: gmx-users@gromacs.org
Sent: Tuesday, 7 December 2010 02:56:04
Subject: [gmx-users] Energy-groups?

Hello,

   I want to plot the interaction potential energy between my solute and 
solvent. In my .mdp file I did not mention anything under energygrps,so I am 
thinking it calculates the energies for the whole system. But is there a way I 
can extract say for example LJ-14 term between my solute and solvent using the 
same .edr file? Or would I have to specify my energygrps and run the simulation 
again.

Thanks.

Nisha

--gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search 
before posting!
Please don't post (un)subscribe requests to the list. Use thewww interface or 
send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] PME energy calculation

[李浩]

Hello Everyone,

I am using PME(4.05) to calculate the long-rang electrostatic interaction,
but when I finished the

Simulation, I found that I can’t get the result of energy of the part of
“fourier space（long range part）”. In other word，there is only a
congregation of energy of that named Coul. recip. Is there any way that I
can get the energy of “group to group” of the “fourier space” ?

Thanks!

   

Li

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] energy_extract

[Mark Abraham]

On 1/07/2011 4:40 PM, balaji nagarajan wrote:

Dear Users !

I have took a penta peptide and did topology generation ,

I have solvated it with water box ,

now i did a minimization with zero step , to know the energy of the 
initial molecule ,


i used g_energy for the out put ,

like

$ g_energy -f em.edr

it gives as follows , i have to type number to get energy !



but it lists Select the terms you want from the following list by
selecting either (part of) the name or the number or a combination.
End your selection with an empty line or a zero.
---
  1  Bond 2  Angle3  Proper-Dih.  4  
Ryckaert-Bell.

  5  LJ-146  Coulomb-14   7  LJ-(SR)  8  LJ-(LR)
  9  Coulomb-(SR)10  Coul.-recip.11  Potential   12  Pressure
 13  Vir-XX  14  Vir-XY  15  Vir-XZ  16  Vir-YX
 17  Vir-YY  18  Vir-YZ  19  Vir-ZX  20  Vir-ZY
 21  Vir-ZZ  22  Pres-XX 23  Pres-XY 24  Pres-XZ
 25  Pres-YX 26  Pres-YY 27  Pres-YZ 28  Pres-ZX
 29  Pres-ZY 30  Pres-ZZ 31  #Surf*SurfTen   32  Mu-X
 33  Mu-Y34  Mu-Z35  T-rest



Is there any way to get the energy of the protein and the energy of 
protein and water alone


There is no way to decompose the existing contents of an .edr file. You 
need to use energy groups (see manual), either in your original 
simulation, or "after the fact" by using mdrun -rerun on your existing 
trajectory with a different .tpr.


Mark
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists