Re: [gmx-users] micelle clustering

[gregory megariotis]

Dear Sulatha, 

You can try the command trjconv -f a.xtc -o
b.gro -pbc cluster -e 0.002 with GROMACS 4.5.4. 

Best regrds 

Grigoris

--- Στις Πέμ., 30/06/11, ο/η sulatha M. S  έγραψε:

Από: sulatha M. S 
Θέμα: [gmx-users] micelle clustering
Προς: "Discussion list for GROMACS users" 
Ημερομηνία: Πέμπτη, 30 Ιούνιος 2011, 9:18





Hi all,
I have simulated a system of randomly dispersed surfactants in
water using gromacs (4.0.7) for about 100 ns MD. Micelles are formed after
around 40 ns.  I am using a time step of
0.002 fs with xtc files written every 500 steps. For analyzing the micellar
properties, I tried the commands given in 

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

and also looked at the various posts given on this topic, (specifically
Chris Neale’s and Tsjerk’s mails).

As posted by Chris Neale, I tried using the commands,

1. trjconv -f a.xtc -o b.gro -pbc cluster -e 0.001 (make sure to just  get one 
frame)2. grompp -f a.mdp -c b.gro -p a.top -o b.tpr3. trjconv -f a.xtc -o b.xtc 
-s b.tpr -pbc nojump


 

Also mentioned in Tsjerk’ post that

“When doing so, be sure to use a frame which is close enough to thestarting 
frame in terms of the coordinates. -pbc nojump works based onthe coordinates 
and if you use a reference which doesn't match the
starting frame close enough everything can get really messed up”.  

I tried the command 1 with 

 trjconv -f a.xtc -o
b.gro -pbc cluster -e 0.002 

and also

 trjconv -f a.xtc -o
b.gro -pbc cluster –dump X (where x=2, 4, 6, 8 etc..)

The program gets into a never ending loop. 

I also tried the command 1 on a later part of the trajectory
(after 40 ns), there also the program enters in a indefinite loop.

I will greatly appreciate any help on how to go about doing
this specifically which frame (for dump or –e argument) .  Please guide me on 
this.

I also downloaded the modified trjconv.c  by Tsjerk (in one of his posts on 
micelle
clustering), but do not know where to incorporate this. I need some help on how
to use this modified trjconv code.
Thanks for any help or clue,
Sulatha



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Re: [gmx-users] micelle clustering

[Tsjerk Wassenaar]

Hi Sulatha,

Did you install gromacs yourself or are you using a system wide
installation?

A. I installed myself

In that case you go into the directory where you have put the gromacs source
code and put the modified version of gmx_trjconv.c in the subdirectory
src/tools. Then you go into that directory and type 'make trjconv'

B. I just used what was available already

If you're good friends with the system administrator you can ask him/her to
compile the modified trjconv, as under A.
Otherwise, you'd better install gromacs yourself as explained on the gromacs
site and then go to A.

Hope it helps,

Tsjerk

On Thu, Jun 30, 2011 at 10:10 AM, gregory megariotis
wrote:

> Dear Sulatha,
>
> You can try the command trjconv -f a.xtc -o b.gro -pbc cluster -e 0.002with 
> GROMACS 4.5.4.
>
> Best regrds
>
> Grigoris
>
> --- Στις *Πέμ., 30/06/11, ο/η sulatha M. S * έγραψε:
>
>
> Από: sulatha M. S 
> Θέμα: [gmx-users] micelle clustering
> Προς: "Discussion list for GROMACS users" 
> Ημερομηνία: Πέμπτη, 30 Ιούνιος 2011, 9:18
>
>
> Hi all,
>
> I have simulated a system of randomly dispersed surfactants in water using
> gromacs (4.0.7) for about 100 ns MD. Micelles are formed after around 40 ns.
>  I am using a time step of 0.002 fs with xtc files written every 500
> steps. For analyzing the micellar properties, I tried the commands given in
>
> http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering
>
> and also looked at the various posts given on this topic, (specifically
> Chris Neale's and Tsjerk's mails).
>
> As posted by Chris Neale, I tried using the commands,
>
> 1. trjconv -f a.xtc -o b.gro -pbc cluster -e 0.001 (make sure to just
>
> get one frame)
>
> 2. grompp -f a.mdp -c b.gro -p a.top -o b.tpr
>
> 3. trjconv -f a.xtc -o b.xtc -s b.tpr -pbc nojump
>
>
>
> Also mentioned in Tsjerk' post that
>
> "When doing so, be sure to use a frame which is close enough to the
>
> starting frame in terms of the coordinates. -pbc nojump works based on
>
> the coordinates and if you use a reference which doesn't match the
>
> starting frame close enough everything can get really messed up".
>
>
>
>
>
> I tried the command 1 with
>
>  trjconv -f a.xtc -o b.gro -pbc cluster -e 0.002
>
> and also
>
>  trjconv -f a.xtc -o b.gro -pbc cluster -dump X (where x=2, 4, 6, 8 etc..)
>
> The program gets into a never ending loop.
>
> I also tried the command 1 on a later part of the trajectory (after 40 ns),
> there also the program enters in a indefinite loop.
>
> I will greatly appreciate any help on how to go about doing this
> specifically which frame (for dump or -e argument) .  Please guide me on
> this.
>
> I also downloaded the modified trjconv.c  by Tsjerk (in one of his posts
> on micelle clustering), but do not know where to incorporate this. I need
> some help on how to use this modified trjconv code.
>
>
> Thanks for any help or clue,
>
> Sulatha
>
>
>
> -Ακολουθεί συνημμένο-
>
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-- 
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
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[gmx-users] the effect of the ligand on each residue

[ahmet yıldırım]

Dear users,

I want to see the effect of the ligand on each residue using the following
command:
g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res

Select group(s) for root mean square calculation
Select a group: ?
Which group should I choose?

Thanks in advance

-- 
Ahmet YILDIRIM
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Re: [gmx-users] the effect of the ligand on each residue

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear users,

I want to see the effect of the ligand on each residue using the 
following command:

g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res

Select group(s) for root mean square calculation
Select a group: ?
Which group should I choose?



The group that is most meaningful to you, based on the behavior observed in the 
trajectory.  You can analyze backbone, sidechain, or all protein atoms 
separately.  Several iterations may be informative, using several different groups.


-Justin

--


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


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Re: [gmx-users] the effect of the ligand on each residue

[ahmet yıldırım]

Dear Justin,

Thanks for your reply. Well, to explore the effect of the ligand on protein

g_mindist -f run.xtc -s run.tpr -od mindist.xvg -on numcont.xvg
Select a group: 1
Selected 1: 'Protein'
Select a group: 13
Selected 13: 'LİGAND'

Does this choice make sense?


30 Haziran 2011 14:43 tarihinde Justin A. Lemkul  yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear users,
>>
>> I want to see the effect of the ligand on each residue using the following
>> command:
>> g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res
>>
>> Select group(s) for root mean square calculation
>> Select a group: ?
>> Which group should I choose?
>>
>>
> The group that is most meaningful to you, based on the behavior observed in
> the trajectory.  You can analyze backbone, sidechain, or all protein atoms
> separately.  Several iterations may be informative, using several different
> groups.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
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> Support/Mailing_Lists/Searchbefore
>  posting!
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>



-- 
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Re: [gmx-users] the effect of the ligand on each residue

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear Justin,

Thanks for your reply. Well, to explore the effect of the ligand on protein

g_mindist -f run.xtc -s run.tpr -od mindist.xvg -on numcont.xvg
Select a group: 1
Selected 1: 'Protein'
Select a group: 13
Selected 13: 'LİGAND'

Does this choice make sense?



Whether or not anything makes sense is up to you.  You have to interpret the 
data you get for your system.  The command is sound, so you probably got output. 
 But as for the applicability or whether or not it makes sense to do this 
analysis is, again, entirely up to you.


-Justin



30 Haziran 2011 14:43 tarihinde Justin A. Lemkul > yazdı:




ahmet yıldırım wrote:

Dear users,

I want to see the effect of the ligand on each residue using the
following command:
g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res

Select group(s) for root mean square calculation
Select a group: ?
Which group should I choose?


The group that is most meaningful to you, based on the behavior
observed in the trajectory.  You can analyze backbone, sidechain, or
all protein atoms separately.  Several iterations may be
informative, using several different groups.

-Justin

-- 
==__==


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


==__==
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 before posting!
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--
Ahmet YILDIRIM


--


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


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[gmx-users] Regarding PDB file

[Ravi Kumar Venkatraman]

Dear All,

 To remove water of crystallization from pdb files. I removed
following things from pdb file.


REMARK   3   SOLVENT ATOMS: 78

.
.

HETATM 1072  O   HOH A 199  16.684  13.594  -5.832  0.31 18.51
O
HETATM 1073  O   HOH A 200  27.534  38.059 -12.862  0.48 18.19
O
HETATM 1074  O   HOH A 201  25.892  35.973  11.563  0.46 18.15
O
HETATM 1075  O   HOH A 202  24.790  25.182  16.063  0.46 17.64
O
HETATM 1076  O   HOH A 203  12.580  21.214   5.006  0.51 17.97
O
HETATM 1077  O   HOH A 204  19.687  23.750  -4.851  0.37 18.08
O
HETATM 1078  O   HOH A 205  27.098  35.956 -12.358  0.39 18.71
O
HETATM 1079  O   HOH A 206  37.255   9.634  10.002  0.46 18.39
O
HETATM 1080  O   HOH A 207  43.755  23.843   8.038  0.38 17.96
O
CONECT   48  981
CONECT  238  889
CONECT  513  630
CONECT  601  724
CONECT  630  513
CONECT  724  601
CONECT  889  238
CONECT  981   48

Is this right or I have to delete some other things also.

Thank you

*With Regards,**
*
*
*
*Ravi Kumar Venkatraman,*
*c/o Prof. Siva Umapathy,**
*
*IPC Dept., IISc.,*
*Bangalore, INDIA.*
*Phone No: +91-9686933963*
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Re: [gmx-users] Regarding PDB file

[Justin A. Lemkul]

Ravi Kumar Venkatraman wrote:

Dear All,

 To remove water of crystallization from pdb files. I 
removed following things from pdb file.



REMARK   3   SOLVENT ATOMS: 78

.
.

HETATM 1072  O   HOH A 199  16.684  13.594  -5.832  0.31 
18.51   O
HETATM 1073  O   HOH A 200  27.534  38.059 -12.862  0.48 
18.19   O
HETATM 1074  O   HOH A 201  25.892  35.973  11.563  0.46 
18.15   O
HETATM 1075  O   HOH A 202  24.790  25.182  16.063  0.46 
17.64   O
HETATM 1076  O   HOH A 203  12.580  21.214   5.006  0.51 
17.97   O
HETATM 1077  O   HOH A 204  19.687  23.750  -4.851  0.37 
18.08   O
HETATM 1078  O   HOH A 205  27.098  35.956 -12.358  0.39 
18.71   O
HETATM 1079  O   HOH A 206  37.255   9.634  10.002  0.46 
18.39   O
HETATM 1080  O   HOH A 207  43.755  23.843   8.038  0.38 
17.96   O

CONECT   48  981
CONECT  238  889
CONECT  513  630
CONECT  601  724
CONECT  630  513
CONECT  724  601
CONECT  889  238
CONECT  981   48

Is this right or I have to delete some other things also.



The only lines you absolutely must remove are the coordinate entries.  REMARK 
and CONECT lines are ignored by pdb2gmx and most other Gromacs programs.


-Justin

--


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


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[gmx-users] rerun confusion

[SebastianWaltz]

Hallo all together,

I am working on a system of a small peptide solvated in CHCl3.
I want to obtain the forces on the peptide atoms  induced by the
solvent. For this I used the rerun option of mdrun_d. I did it now in
two ways:
1st: using trjconv to get the pure peptide trajectory. When using the
rerun option with no special configurations of the .mdp file. If the
obtained force are pair additive I should get the wanted result if I
subtract from the forces of the original trajectory the rerun forces.
2nd: using the original trajectory and changing the options of the .mdp
file as follows:
energygrps  =  Protein SOL
energygrp_excl=  Protein Protein SOL SOL
and changing the coulomb type to Cut-off because of the separation
problem using PME.

Comparing this two results I realize that they are totally different.
There is no correlation to detect between this two.
I am wondering now which way to go to get the correct answer for my
question. I probably just do not understand the energygrps and
energygrp_excl option right.
Using rerun with the same trajectory and the same .mdp option except
changing PME to Cut-off gives the same result as the original trajectory
or at least up to the last 3 decimal places of a double value.

I would be really happy if someone can help me

Thanks a lot

Sebastian  
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[gmx-users] pdb2gmx

[simon sham]

Hi,
I have a question about pdb2gmx. If a pdb file contains a multiple structures, 
will it average the coordinates or just pick one of the structures to convert?

Thanks for your insight.

Simon
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Re: [gmx-users] pdb2gmx

[Tsjerk Wassenaar]

Hi Simon,

pdb2gmx takesthe first structure. Taking an average would ba awkward, as it
is unlikely to correspond to a real structure.

Cheers,

Tsjerk

On Jun 30, 2011 6:02 PM, "simon sham"  wrote:

Hi,
I have a question about pdb2gmx. If a pdb file contains a multiple
structures, will it average the coordinates or just pick one of the
structures to convert?

Thanks for your insight.

Simon

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[gmx-users] Calculate distance between two atoms

[Amjad Farooq]

Hello everyone,

I would like to calculate distance between two atoms from an MD run. For 
example, how do I probe changes in distance between CD atom of Pro23 and OE1 
atom of Glu75 as a function of simulation time.

From the manual, I understand that one should use the command g_dist that 
includes the index.ndx file. My questions are:

(1) How do I create an index.ndx file for the the above-mentioned pair of atoms?
(2) What is the exact format of g_dist that should be applied on the command 
line?

Thank you very much for your help!
Amjad
 

AMJAD FAROOQ PhD DIC
Associate Professor and Laboratory Head
Farooq Laboratory of Macromolecular Biophysics, Gautier Bldg #217/219
Dept of Biochemistry & Molecular Biology and USylvester Braman Family Breast 
Cancer Institute
Leonard Miller School of Medicine, University of Miami, Miami, FL 33136

1011 NW 15th Street #217, Miami, FL 33136 (Mailing Address)
a.far...@miami.edu | am...@farooqlab.net | amjadfar...@yahoo.com
off 305-243-2429 | lab 305-243-9799 | fax 305-243-3955 
www.farooqlab.net 
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Re: [gmx-users] Installation of gromacs-gpu on windows

[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
> --
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Re: [gmx-users] Calculate distance between two atoms

[Justin A. Lemkul]

Amjad Farooq wrote:

Hello everyone,

I would like to calculate distance between two atoms from an MD run. For 
example, how do I probe changes in distance between CD atom of Pro23 and 
OE1 atom of Glu75 as a function of simulation time.


 From the manual, I understand that one should use the command g_dist 
that includes the index.ndx file. My questions are:


(1) How do I create an index.ndx file for the the above-mentioned pair 
of atoms?


Use make_ndx.  Type 'help' at the prompt for examples.  For indices with just 
one atom each this is not strictly necessary; you can create the necessary 
groups with a text editor.


(2) What is the exact format of g_dist that should be applied on the 
command line?




Please read g_dist -h.

-Justin

--


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


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[gmx-users] g_velacc

[Nilesh Dhumal]

Hello,

I am trying to calcualte 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 geting 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









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Re: [gmx-users] rerun confusion

[Mark Abraham]

On 1/07/2011 1:57 AM, SebastianWaltz wrote:

Hallo all together,

I am working on a system of a small peptide solvated in CHCl3.
I want to obtain the forces on the peptide atoms  induced by the
solvent. For this I used the rerun option of mdrun_d. I did it now in
two ways:
1st: using trjconv to get the pure peptide trajectory. When using the
rerun option with no special configurations of the .mdp file. If the
obtained force are pair additive I should get the wanted result if I
subtract from the forces of the original trajectory the rerun forces.


Not necessarily. Reruns do neighbour searching every frame, which you 
may not have been doing in the original trajectory. Obviously, you'll 
need to omit all the solvent atoms after the subtraction.



2nd: using the original trajectory and changing the options of the .mdp
file as follows:
energygrps  =  Protein SOL
energygrp_excl=  Protein Protein SOL SOL
and changing the coulomb type to Cut-off because of the separation
problem using PME.

Comparing this two results I realize that they are totally different.
There is no correlation to detect between this two.


If the first used PME and rcoulomb is the same, then this is expected.


I am wondering now which way to go to get the correct answer for my
question. I probably just do not understand the energygrps and
energygrp_excl option right.


The way you are using them above is correct. However, your two 
approaches should give the same results if you use the same 
electrostatics regime for both reruns.



Using rerun with the same trajectory and the same .mdp option except
changing PME to Cut-off gives the same result as the original trajectory
or at least up to the last 3 decimal places of a double value.


That's inconceivable for well-formed PME. I think you may be mismatching 
files.


Mark


I would be really happy if someone can help me

Thanks a lot

Sebastian


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[gmx-users] terminal_fixing

[balaji nagarajan]

Dear Users ! 

i have tried in generating the -ter option in generating the topology file ! 

it asks the below if i give the ter option , 

Select start terminus type for TYR-1
 0: NH3+
 1: ZWITTERION_NH3+
 2: NH2
 3: None

then if  i give option 1 it chooses  ZWITTERION_NH3+ , i want to make the 
charge state of the protein as  ZWITTERION , in terminal how to do it in 
command mode 


thanks in advance 
balaji

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Re: [gmx-users] terminal_fixing

[Justin A. Lemkul]

balaji nagarajan wrote:

Dear Users !

i have tried in generating the -ter option in generating the topology 
file !


it asks the below if i give the ter option ,

Select start terminus type for TYR-1
 0: NH3+
 1: ZWITTERION_NH3+
 2: NH2
 3: None

then if  i give option 1 it chooses  ZWITTERION_NH3+ , i want to make 
the charge state of the protein as  ZWITTERION , in terminal how to do 
it in command mode





The zwitterion option should only be invoked in the case of a single, 
zwitterionic amino acid.  For any polypeptide you should choose normal termini 
(NH3+ and COO- in your case).  If you choose the zwitterion forms, your topology 
will be broken.


-Justin

--


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


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[gmx-users] g_velacc

[Nilesh Dhumal]

Hello,

I am trying to calcualte 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 geting 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









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Re: [gmx-users] Re: local pressure v4.5 issues

[Amit Choubey]

Hello Everyone,

The  git version of local pressure calculation at

http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

is broken. I could not get it to work for my simulations.

I installed gromacs local pressure version 4.0 from

ftp://ftp.gromacs.org/pub/tmp/

I used 
gromacs-4.0.2_localpressure.tar.gz
in
that folder.

The pressure values printed using this version seem reasonable to me. I
converted all the tpr files from v 4.5 to v 4.0.

The output of the mdrun in v 4.0 is a single file "localpressure.dat" . On
the contrary in v 4.5 there were separate "localpressure.dat*" files for
each frame.

I am not sure what exactly is the content of "localpressure.dat". Does it
have the time averaged value of pressure tensor for each voxel ? It doesnt
seem so to me because i tried it over only two frames (3 reruns were done
for two frames separately and a .trr which had these two frames only) and
the numbers did not seem to be averages.

Can someone help me in figuring out what is going on ?

Amit

On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey  wrote:

>
>
> On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li  wrote:
>
>> Hi Amit,
>>
>> May I ask you a question?
>> In your calculation of local pressure using a trajectory file, did you get
>> a single averaged localpressure.dat file? Or else you get a bunch of
>> separate files for each frame (e.g., localpressure.dat0, localpressure.dat1,
>> localpressure.dat2 )?
>>
>
> Yes I do get different files for different trajectories. All the files seem
> to have the same problem ie a very large/small number printed as tensor
> elements of the pressure for some of the voxels.
>
> Do you have such problems ? Could we compare our methodologies to use the
> local pressure version ?
>
> Amit
>
>>
>> Thank you very much!
>>
>> Cheers,
>> Jianguo
>>
>>
>> --
>> *From:* Amit Choubey 
>> *To:* Discussion list for GROMACS users 
>> *Sent:* Monday, 20 June 2011 07:08:03
>> *Subject:* [gmx-users] Re: local pressure v4.5 issues
>>
>> Dear all,
>>
>> I did another simulation with only SPC water. Then I used the local
>> pressure gromacs to calculate the stresses. It seems to be reasonable.
>>
>> I am not sure how to figure out what goes wrong with my previous
>> simulations when plugged into the local pressure gromacs.
>>
>> Could someone help me in figuring out whats the issue ?
>>
>> Thank You.
>>
>> On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey  wrote:
>>
>>> Dear all,
>>>
>>> I installed the git version of local pressure calculation from
>>>
>>>
>>> http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
>>>
>>> The I invoked mdrun
>>>
>>> mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid
>>> 0.1
>>>
>>> This created a file named "localpressure.dat0". This is a binary file so
>>> I could not look at it directly. I am not sure if there is a tool in the
>>> gromacs to look at it directly.
>>>
>>> To look at the data in "localpressure.dat0" I used the planar_av.c code
>>> available in "pressure-tools" folder at
>>>
>>> http://md.chem.rug.nl/cgmartini/index.php/3d
>>>
>>> When I look at the Pressure tensor averaged over xy plane, some of the
>>> numbers are reasonable but few of them are ridiculously large numbers which
>>> is not expected.
>>>
>>> I checked this on two different simulations and I got the same problems.
>>> The simulations had run OK previously.
>>>
>>> Could someone help me in figuring our whats going on ?
>>>
>>> Amit Choubey
>>>
>>>
>>
>
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Re: [gmx-users] Re: local pressure v4.5 issues

[Jianguo Li]

Hi Amit,

I also encountered the same problem you mentioned.
In v4.5, when using -nstlp wiht large value (e.g., 1000), I got one file 
"localpressure.dat0". I tested first several frames of a trajectory, the 
calculated pressure is not the average of the pressure of individual frames. 

 
Btw, did you use CHARMM FF in your simulations and how did you convert the tpr 
files from v 4.5 to v 4.0?


Cheers
Jianguo





From: Amit Choubey 
To: Jianguo Li ; Discussion list for GROMACS users 

Sent: Friday, 1 July 2011 10:32:07
Subject: Re: [gmx-users] Re: local pressure v4.5 issues

Hello Everyone,

The  git version of local pressure calculation at 


http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

is broken. I could not get it to work for my simulations.

I installed gromacs local pressure version 4.0 from

ftp://ftp.gromacs.org/pub/tmp/

I used gromacs-4.0.2_localpressure.tar.gz in that folder. 

The pressure values printed using this version seem reasonable to me. I 
converted all the tpr files from v 4.5 to v 4.0.

The output of the mdrun in v 4.0 is a single file "localpressure.dat" . On the 
contrary in v 4.5 there were separate "localpressure.dat*" files for each 
frame. 

I am not sure what exactly is the content of "localpressure.dat". Does it have 
the time averaged value of pressure tensor for each voxel ? It doesnt seem so 
to 
me because i tried it over only two frames (3 reruns were done for two frames 
separately and a .trr which had these two frames only) and the numbers did not 
seem to be averages.

Can someone help me in figuring out what is going on ?
Amit

On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey  wrote:


>
>
>On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li  wrote:
>
>Hi Amit,
>>
>>May I ask you a question? 
>>In your calculation of local pressure using a trajectory file, did you get a 
>>single averaged localpressure.dat file? Or else you get a bunch of separate 
>>files for each frame (e.g., localpressure.dat0, localpressure.dat1, 
>>localpressure.dat2 )?
>>

>Yes I do get different files for different trajectories. All the files seem to 
>have the same problem ie a very large/small number printed as tensor elements 
>of 
>the pressure for some of the voxels.
>
>
>Do you have such problems ? Could we compare our methodologies to use the 
>local 
>pressure version ?
>
>Amit
>
>>Thank you very much!
>>
>>Cheers,
>>Jianguo
>>
>>
>>
>>
>>

From: Amit Choubey 
>>To: Discussion list for GROMACS users 
>>Sent: Monday, 20 June 2011 07:08:03
>>Subject: [gmx-users] Re: local pressure v4.5 issues
>>
>>
>>Dear all,
>>
>>
>>I did another simulation with only SPC water. Then I used the local pressure 
>>gromacs to calculate the stresses. It seems to be reasonable. 
>>
>>
>>I am not sure how to figure out what goes wrong with my previous simulations 
>>when plugged into the local pressure gromacs.
>>
>>
>>Could someone help me in figuring out whats the issue ?
>>
>>
>>Thank You.
>>
>>
>>On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey  wrote:
>>
>>Dear all,
>>>
>>>I installed the git version of local pressure calculation from 
>>>
>>>http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
>>>
>>>The I invoked mdrun
>>>
>>>mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid 0.1
>>>
>>>This created a file named "localpressure.dat0". This is a binary file so I 
>>>could 
>>>not look at it directly. I am not sure if there is a tool in the gromacs to 
>>>look 
>>>at it directly. 
>>>
>>>
>>>To look at the data in "localpressure.dat0" I used the planar_av.c code 
>>>available in "pressure-tools" folder at
>>>
>>>http://md.chem.rug.nl/cgmartini/index.php/3d
>>>
>>>When I look at the Pressure tensor averaged over xy plane, some of the 
>>>numbers 
>>>are reasonable but few of them are ridiculously large numbers which is not 
>>>expected. 
>>>
>>>
>>>I checked this on two different simulations and I got the same problems. The 
>>>simulations had run OK previously.
>>>
>>>Could someone help me in figuring our whats going on ?
>>>
>>>Amit Choubey
>>>
>>>
>>
>
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Re: [gmx-users] Re: local pressure v4.5 issues

[Amit Choubey]

On Thu, Jun 30, 2011 at 7:57 PM, Jianguo Li  wrote:

> Hi Amit,
>
> I also encountered the same problem you mentioned.
> In v4.5, when using -nstlp wiht large value (e.g., 1000), I got one
> file "localpressure.dat0". I tested first several frames of a trajectory,
> the calculated pressure is not the average of the pressure of individual
> frames.
>
>

In v4.5 it outputs the profile for frames in separate files which is ok. My
concern is what exactly is going in v 4.0 where there is only one file for
all the frames.

Also where did you download v4.5 and v4.0 from ?


> Btw, did you use CHARMM FF in your simulations and how did you convert the
> tpr files from v 4.5 to v 4.0?
>

Yes i have used CHARMM FF and i will have to figure out the conversion.

>
> Cheers
> Jianguo
>
> --
> *From:* Amit Choubey 
> *To:* Jianguo Li ; Discussion list for GROMACS users
> 
> *Sent:* Friday, 1 July 2011 10:32:07
> *Subject:* Re: [gmx-users] Re: local pressure v4.5 issues
>
> Hello Everyone,
>
> The  git version of local pressure calculation at
>
>
> http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
>
> is broken. I could not get it to work for my simulations.
>
> I installed gromacs local pressure version 4.0 from
>
> ftp://ftp.gromacs.org/pub/tmp/
>
> I used 
> gromacs-4.0.2_localpressure.tar.gz
>  in
> that folder.
>
> The pressure values printed using this version seem reasonable to me. I
> converted all the tpr files from v 4.5 to v 4.0.
>
> The output of the mdrun in v 4.0 is a single file "localpressure.dat" . On
> the contrary in v 4.5 there were separate "localpressure.dat*" files for
> each frame.
>
> I am not sure what exactly is the content of "localpressure.dat". Does it
> have the time averaged value of pressure tensor for each voxel ? It doesnt
> seem so to me because i tried it over only two frames (3 reruns were done
> for two frames separately and a .trr which had these two frames only) and
> the numbers did not seem to be averages.
>
> Can someone help me in figuring out what is going on ?
>
> Amit
>
> On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey  wrote:
>
>>
>>
>> On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li  wrote:
>>
>>> Hi Amit,
>>>
>>> May I ask you a question?
>>> In your calculation of local pressure using a trajectory file, did you
>>> get a single averaged localpressure.dat file? Or else you get a bunch of
>>> separate files for each frame (e.g., localpressure.dat0, localpressure.dat1,
>>> localpressure.dat2 )?
>>>
>>
>> Yes I do get different files for different trajectories. All the files
>> seem to have the same problem ie a very large/small number printed as tensor
>> elements of the pressure for some of the voxels.
>>
>> Do you have such problems ? Could we compare our methodologies to use the
>> local pressure version ?
>>
>> Amit
>>
>>>
>>> Thank you very much!
>>>
>>> Cheers,
>>> Jianguo
>>>
>>>
>>> --
>>> *From:* Amit Choubey 
>>> *To:* Discussion list for GROMACS users 
>>> *Sent:* Monday, 20 June 2011 07:08:03
>>> *Subject:* [gmx-users] Re: local pressure v4.5 issues
>>>
>>> Dear all,
>>>
>>> I did another simulation with only SPC water. Then I used the local
>>> pressure gromacs to calculate the stresses. It seems to be reasonable.
>>>
>>> I am not sure how to figure out what goes wrong with my previous
>>> simulations when plugged into the local pressure gromacs.
>>>
>>> Could someone help me in figuring out whats the issue ?
>>>
>>> Thank You.
>>>
>>> On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey wrote:
>>>
 Dear all,

 I installed the git version of local pressure calculation from


 http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure

 The I invoked mdrun

 mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid
 0.1

 This created a file named "localpressure.dat0". This is a binary file so
 I could not look at it directly. I am not sure if there is a tool in the
 gromacs to look at it directly.

 To look at the data in "localpressure.dat0" I used the planar_av.c code
 available in "pressure-tools" folder at

 http://md.chem.rug.nl/cgmartini/index.php/3d

 When I look at the Pressure tensor averaged over xy plane, some of the
 numbers are reasonable but few of them are ridiculously large numbers which
 is not expected.

 I checked this on two different simulations and I got the same problems.
 The simulations had run OK previously.

 Could someone help me in figuring our whats going on ?

 Amit Choubey


>>>
>>
>
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Re: [gmx-users] Re: local pressure v4.5 issues

[Jianguo Li]

I downloaded v4.5 and v4.0 from the same websites as you mentioned in previous 
email. I am not sure why v4.5 give inconsistent results. I haven't try v4.0, 
because my simulation is using CHARMM FF. Could you give more details of 
conversion tpr files from v4.5 to v4.0 using CHARMM FF?
Thank you very much!

Cheers,
Jianguo







From: Amit Choubey 
To: Jianguo Li 
Cc: Discussion list for GROMACS users 
Sent: Friday, 1 July 2011 11:47:58
Subject: Re: [gmx-users] Re: local pressure v4.5 issues




On Thu, Jun 30, 2011 at 7:57 PM, Jianguo Li  wrote:

Hi Amit,
>
>I also encountered the same problem you mentioned.
>In v4.5, when using -nstlp wiht large value (e.g., 1000), I got one file 
>"localpressure.dat0". I tested first several frames of a trajectory, the 
>calculated pressure is not the average of the pressure of individual frames. 
>
> 
>

In v4.5 it outputs the profile for frames in separate files which is ok. My 
concern is what exactly is going in v 4.0 where there is only one file for all 
the frames.

Also where did you download v4.5 and v4.0 from ?
 
Btw, did you use CHARMM FF in your simulations and how did you convert the tpr 
files from v 4.5 to v 4.0?
>

Yes i have used CHARMM FF and i will have to figure out the conversion. 

>
>Cheers
>Jianguo
>
>
>
>

From: Amit Choubey 
>To: Jianguo Li ; Discussion list for GROMACS users 
>
>Sent: Friday, 1 July 2011 10:32:07
>Subject: Re: [gmx-users] Re: local pressure v4.5 issues
>
>
>Hello Everyone,
>
>
>The  git version of local pressure calculation at 
>
>
>http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure
>
>
>is broken. I could not get it to work for my simulations.
>
>
>I installed gromacs local pressure version 4.0 from
>
>
>ftp://ftp.gromacs.org/pub/tmp/
>
>
>I used gromacs-4.0.2_localpressure.tar.gz in that folder. 
>
>
>The pressure values printed using this version seem reasonable to me. I 
>converted all the tpr files from v 4.5 to v 4.0.
>
>
>The output of the mdrun in v 4.0 is a single file "localpressure.dat" . On the 
>contrary in v 4.5 there were separate "localpressure.dat*" files for each 
>frame. 
>
>
>I am not sure what exactly is the content of "localpressure.dat". Does it have 
>the time averaged value of pressure tensor for each voxel ? It doesnt seem so 
>to 
>me because i tried it over only two frames (3 reruns were done for two frames 
>separately and a .trr which had these two frames only) and the numbers did not 
>seem to be averages.
>
>
>Can someone help me in figuring out what is going on ?
>
>Amit
>
>On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey  wrote:
>
>
>>
>>
>>On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li  wrote:
>>
>>Hi Amit,
>>>
>>>May I ask you a question? 
>>>In your calculation of local pressure using a trajectory file, did you get a 
>>>single averaged localpressure.dat file? Or else you get a bunch of separate 
>>>files for each frame (e.g., localpressure.dat0, localpressure.dat1, 
>>>localpressure.dat2 )?
>>>
>
>
>>Yes I do get different files for different trajectories. All the files seem 
>>to 
>>have the same problem ie a very large/small number printed as tensor elements 
>>of 
>>the pressure for some of the voxels.
>>
>>
>>Do you have such problems ? Could we compare our methodologies to use the 
>>local 
>>pressure version ?
>>
>>Amit
>>
>>>Thank you very much!
>>>
>>>Cheers,
>>>Jianguo
>>>
>>>
>>>
>>>
>>>

From: Amit Choubey 
>>>To: Discussion list for GROMACS users 
>>>Sent: Monday, 20 June 2011 07:08:03
>>>Subject: [gmx-users] Re: local pressure v4.5 issues
>>>
>>>
>>>Dear all,
>>>
>>>
>>>I did another simulation with only SPC water. Then I used the local pressure 
>>>gromacs to calculate the stresses. It seems to be reasonable. 
>>>
>>>
>>>I am not sure how to figure out what goes wrong with my previous simulations 
>>>when plugged into the local pressure gromacs.
>>>
>>>
>>>Could someone help me in figuring out whats the issue ?
>>>
>>>
>>>Thank You.
>>>
>>>
>>>On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey  wrote:
>>>
>>>Dear all,

I installed the git version of local pressure calculation from 

http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure


The I invoked mdrun

mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid 0.1

This created a file named "localpressure.dat0". This is a binary file so I 
could 
not look at it directly. I am not sure if there is a tool in the gromacs to 
look 
at it directly. 


To look at the data in "localpressure.dat0" I used the planar_av.c code 
available in "pressure-tools" folder at

http://md.chem.rug.nl/cgmartini/index.php/3d

When I look at the Pressure tensor averaged over xy plane, some of the 
numbers 
are reasonable but few of them are ridiculously large numbers which is not 
expected.

Re: [gmx-users] micelle clustering

[sulatha M. S]

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. 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?

make trjconv
/bin/sh ../../libtool --tag=CC   --mode=compile cc -DHAVE_CONFIG_H -I.
-I../../src -I/usr/include/libxml2 -I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\"   -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_trjconv.lo
-MD -MP -MF .deps/gmx_trjconv.Tpo -c -o gmx_trjconv.lo gmx_trjconv.c
 cc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_trjconv.lo
-MD -MP -MF .deps/gmx_trjconv.Tpo -c gmx_trjconv.c -o gmx_trjconv.o
gmx_trjconv.c: In function 'taw_pbc_cluster':
gmx_trjconv.c:91: error: 'gmx_bool' undeclared (first use in this function)
gmx_trjconv.c:91: error: (Each undeclared identifier is reported only once
gmx_trjconv.c:91: error: for each function it appears in.)
gmx_trjconv.c:91: error: expected ';' before 'bClustered'
gmx_trjconv.c:148: error: 'bClustered' undeclared (first use in this
function)
gmx_trjconv.c: In function 'calc_pbc_cluster':
gmx_trjconv.c:214: error: 'gmx_bool' undeclared (first use in this function)
gmx_trjconv.c:214: error: expected ';' before 'bChanged'
gmx_trjconv.c:220: error: 'bMol' undeclared (first use in this function)
gmx_trjconv.c:220: error: 'bTmp' undeclared (first use in this function)
gmx_trjconv.c:333: error: 'bChanged' undeclared (first use in this function)
gmx_trjconv.c: In function 'put_residue_com_in_box':
gmx_trjconv.c:442: error: 't_atom' has no member named 'resind'
gmx_trjconv.c:465: error: 't_atom' has no member named 'resind'
gmx_trjconv.c:483: error: 't_atom' has no member named 'resind'
gmx_trjconv.c: In function 'do_trunc':
gmx_trjconv.c:542: error: 't_fileio' undeclared (first use in this function)
gmx_trjconv.c:542: error: 'in' undeclared (first use in this function)
gmx_trjconv.c:544: error: 'gmx_bool' undeclared (first use in this function)
gmx_trjconv.c:544: error: expected ';' before 'bStop'
gmx_trjconv.c:546: error: 'gmx_off_t' undeclared (first use in this
function)
gmx_trjconv.c:546: error: expected ';' before 'fpos'
gmx_trjconv.c:557: warning: passing argument 1 of 'open_trn' discards
qualifiers from pointer target type
gmx_trjconv.c:564: error: 'fpos' undeclared (first use in this function)
gmx_trjconv.c:565: error: 'bStop' undeclared (first use in this function)
gmx_trjconv.c:566: error: 'bOK' undeclared (first use in this function)
gmx_trjconv.c:568: warning: implicit declaration of function 'gmx_ftell'
gmx_trjconv.c:571: warning: implicit declaration of function 'gmx_fseek'
gmx_trjconv.c: In function 'gmx_trjconv':
gmx_trjconv.c:758: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'bAppend'
gmx_trjconv.c:758: error: 'bAppend' undeclared (first use in this function)
gmx_trjconv.c:758: error: 'bSeparate' undeclared (first use in this
function)
gmx_trjconv.c:758: error: 'bVels' undeclared (first use in this function)
gmx_trjconv.c:758: error: 'bForce' undeclared (first use in this function)
gmx_trjconv.c:758: error: 'bCONECT' undeclared (first use in this function)
gmx_trjconv.c:759: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'bCenter'
gmx_trjconv.c:759: error: 'bCenter' undeclared (first use in this function)
gmx_trjconv.c:765: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'bRound'
gmx_trjconv.c:765: error: 'bRound' undeclared (first use in this function)
gmx_trjconv.c:855: error: 't_trxstatus' undeclared (first use in this
function)
gmx_trjconv.c:855: error: 'trxout' undeclared (first use in this function)
gmx_trjconv.c:855: error: invalid operands to binary *
gmx_trjconv.c:856: error: 'status' undeclared (first use in this function)
gmx_trjconv.c:856: error: invalid operands to binary *
gmx_trjconv.c:878: error: 'clust_status' undeclared (first use in this
function)
gmx_trjconv.c:878: error: invalid operands to binary *
gmx_trjconv.c:885: error: 'gmx_bool' undeclared (first use in this function)
gmx_trjconv.c:885: error: expected ';' before 'bFit'
gmx_trjconv.c:887: error: 'gmx_rmpbc_t' undeclared (first use in this
function)
gmx_trjconv.c:887: error: expected ';' before 'gpbc'
gmx_trjconv.c:888: error: expected ';' before 'bRmPBC'
gmx_trjconv.c:889: error: expected ';' before 'bCopy'
gmx_trjconv.c:890: error: expected ';' before 'bExec'
gmx_trjconv.c:891: error: expected ';' before 'bHaveFirstFrame'
gmx_trjconv.c:892: error: expected ';' before 'bSubTraj'
gmx_trjconv.c:893: error: expe

Re: [gmx-users] micelle clustering

[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

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Re: [gmx-users] micelle clustering

[sulatha M. S]

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

[balaji nagarajan]

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 

I dont need water water interactions ! 



how to do this ! 

thanks in advance 




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