Re: [gmx-users] Interaction energy between specific residue in a set of residues

[Justin Lemkul]

On 7/31/13 4:20 PM, Collins Nganou wrote:

Dear all,

I am looking how  I can extract the interaction energy between  specific
residue in a set of  residues.



Nonbonded energy terms are decomposed using energygrps in the .mdp file along 
with suitable index groups.



example:

I have DT and DA residues, I would like to plot only the energy of the DT.
I can extract the DT with the index file, But I am missing information on
how to plot the energy base on my index file where I can select only DT.



You can create index groups for any base or bases you want individually.  You 
haven't shown us what you've done, so it's hard to critique beyond that.



I was only looking the way to extract the c5-c6 distance of adjacent DT
without include DA.



Distances are calculated with g_dist and suitable index groups.

-Justin

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[gmx-users] Interaction energy between specific residue in a set of residues

[Collins Nganou]

Dear all,

I am looking how  I can extract the interaction energy between  specific
residue in a set of  residues.

example:

I have DT and DA residues, I would like to plot only the energy of the DT.
I can extract the DT with the index file, But I am missing information on
how to plot the energy base on my index file where I can select only DT.

I was only looking the way to extract the c5-c6 distance of adjacent DT
without include DA.

I will be very grateful to receive any suggestions



I wish you all a wonderful day...

Collins
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Re: [gmx-users] interaction energy using g_enemat

[Justin Lemkul]

On 7/24/13 7:47 AM, Poojari, Chetan wrote:

Dear All,

I want to calculate interaction energy per residue.

Below is the command i used:

g_enemat -f strand.edr -groups groups.dat -emat strand_emat.xpm


my groups.dat file contains these lines:

3
strand1_SER_34
strand1_THR_36
strand1_TYR_37


When i execute the above g_enemat command i get the below error message:

WARNING! could not find group LJ-SR:strand1_SER_34 -strand1_THR_36  (34,36)in 
energy file
WARNING! could not find group Coul-SR:strand1_SER_34 -strand1_TYR_37  (34,37)in 
energy file


My strand.edr file looks like this:

LJ-SR:strand1_SER_34-strand1_THR_36
Coul-SR:strand1_SER_34-strand1_TYR_37



Please can I get some suggestions on how to get around this problem.



I think g_enemat is buggy.  People post the same issue or slight variants of it 
all the time.  My version 4.6 installation fares even worse, as group names 
aren't even recognized (set to 'null' for everything).


You can get interaction energies over time using g_energy, but I don't think 
g_enemat currently functions properly.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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[gmx-users] interaction energy using g_enemat

[Poojari, Chetan]

Dear All,

I want to calculate interaction energy per residue.

Below is the command i used:

g_enemat -f strand.edr -groups groups.dat -emat strand_emat.xpm


my groups.dat file contains these lines:

3
strand1_SER_34
strand1_THR_36
strand1_TYR_37


When i execute the above g_enemat command i get the below error message:

WARNING! could not find group LJ-SR:strand1_SER_34 -strand1_THR_36  (34,36)in 
energy file
WARNING! could not find group Coul-SR:strand1_SER_34 -strand1_TYR_37  (34,37)in 
energy file


My strand.edr file looks like this:

LJ-SR:strand1_SER_34-strand1_THR_36
Coul-SR:strand1_SER_34-strand1_TYR_37



Please can I get some suggestions on how to get around this problem.


Kind Regards,
Chetan




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Re: [gmx-users] interaction energy

[Justin Lemkul]

On 4/18/13 2:00 AM, fatemeh ramezani wrote:



  HI
I'm simulating gold-protein interaction by gromacs. after MD simulation I want 
to calculate interaction energy of each aminoacids with

AU surface.
Enon-bond = E(vdw) + E(elec)


gold atoms  charge in simulation were considered 0, then E non-bonded=E(vdw)
Is this true?
The interaction energy is equal to the van der Waals energy?



If charges are zero, then yes.

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
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] interaction energy

[fatemeh ramezani]

 HI
I'm simulating gold-protein interaction by gromacs. after MD simulation I want 
to calculate interaction energy of each aminoacids with 

AU surface. 
Enon-bond = E(vdw) + E(elec) 


gold atoms  charge in simulation were considered 0, then E non-bonded=E(vdw)
Is this true?
The interaction energy is equal to the van der Waals energy?


Fatemeh Ramezani
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Re: [gmx-users] Interaction energy between two molecules.

[Justin Lemkul]

On 12/2/12 10:38 PM, Mortuza Munna wrote:

Dear Gromacs User, I am simulating two constrained fullerenes to analyze the
interaction energy between these two in vacuum. To do that I specified
energygrps in .mdp file as CB1 and CB2 which corrospond to the residue name
of first and second fullerene respectively. The charge of the atoms of
fullerenes are zero. Therefore, only the LJ-SR of CB1-CB2 should be the total
interaction energy between these two. My understanding is, this total
interaction energy is the combination of both attractive and repulsive term
of Lennard-Jones potential. Is there anyway to find only the attraction
energy (-C6/r^6) which is contributing to this total interaction energy
between these two fullerenes? Or, in other words I would like to know the
attractive energy (-C6/r^6) between these two fullerenes. I would really
appreciate if anyone can help me.



The approach that comes to mind is to create a custom topology in which the 
relevant C6 or C12 parameters are alternatively set to zero.  You can then 
create new .tpr files that have either only attractive or only repulsive terms. 
 Then use the mdrun -rerun feature with this new .tpr file and the existing 
trajectory file to have the energies recalculated.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Interaction energy between two molecules.

[Mortuza Munna]

Dear Gromacs User,
I am simulating two constrained fullerenes to analyze the interaction energy 
between these two in vacuum. To do that I specified energygrps in .mdp file as 
CB1 and CB2 which corrospond to the residue name of first and second fullerene 
respectively. The charge of the atoms of fullerenes are zero. Therefore, only 
the LJ-SR of CB1-CB2 should be the total interaction energy between these two. 
My understanding is, this total interaction energy is the combination of both 
attractive and repulsive term of Lennard-Jones potential. Is there anyway to 
find only the attraction energy (-C6/r^6) which is contributing to this total 
interaction energy between these two fullerenes? Or, in other words I would 
like to know the attractive energy (-C6/r^6) between these two fullerenes. I 
would really appreciate if anyone can help me.


Thanks in advance.

 
Regards,
Mortuza

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Re: [gmx-users] Interaction energy..

[Justin Lemkul]

On 10/8/12 7:09 AM, rama david wrote:

Hi justin,


g_enemat -f ener.edr -groups groups.dat -coul -nolj


Out-put is like

Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 3 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames
Segmentation fault (core dumped)



At this point, I honestly have no idea why it's not working.  If you want me to 
try to debug the issue a bit, you can send me the .edr file (off-list) if it can 
be sent via email.  If it is too large of a file, use eneconv to cut down some 
frames.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Interaction energy..

[rama david]

Hi justin,


g_enemat -f ener.edr -groups groups.dat -coul -nolj


Out-put is like

Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 3 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames
Segmentation fault (core dumped)


Thank you in advance
Rama david.

>
>>
> Let me be a bit more specific again.  I previously suggested there was a
> problem with the -lj flag activating more than one option in the code, so
> that is a potential problem.  I suggested adding -nolj -coul to test this
> theory.  Please use those options (not -coul -lj) and see what happens.
>
> -Justin
>
>
>> On Mon, Oct 8, 2012 at 3:22 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 10/8/12 5:40 AM, rama david wrote:
>>>
>>>  Hi justin,

 As per your advice,

g_enemat -f ener.edr -groups groups.dat -nocoul -nolj


 Opened ener.edr as single precision energy file
 Will read groupnames from inputfile
 Read 2 groups
 group 0WARNING! could not find group (null):energy-energy (0,0)in energy
 file
 WARNING! could not find group (null):energy-extra34 (0,1)in energy file
 group 1WARNING! could not find group (null):extra34-extra34 (1,1)in
 energy
 file

 Will select half-matrix of energies with 0 elements
 Last energy frame read 5 time 1.000
 Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames
 Segmentation fault (core dumped)

 What is the reason  ???


  I told you to add the -coul flag, not -nocoul.  With the above command,
>>> you're explicitly telling g_enemat to not do anything useful.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ====
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ====
>>>
>>> --
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>>> http://www.gromacs.org/Support/Mailing_Lists
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>>> >
>>>
>>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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] Interaction energy..

[Justin Lemkul]

On 10/8/12 6:00 AM, rama david wrote:

Hi justin,
I correct command as follow and
  g_enemat -f ener.edr -groups groups.dat -coul -lj

out-put is like


Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 9 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 9 elements, over 50001 frames
Segmentation fault (core dumped)



Let me be a bit more specific again.  I previously suggested there was a problem 
with the -lj flag activating more than one option in the code, so that is a 
potential problem.  I suggested adding -nolj -coul to test this theory.  Please 
use those options (not -coul -lj) and see what happens.


-Justin



On Mon, Oct 8, 2012 at 3:22 PM, Justin Lemkul  wrote:




On 10/8/12 5:40 AM, rama david wrote:


Hi justin,

As per your advice,

   g_enemat -f ener.edr -groups groups.dat -nocoul -nolj


Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 0 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames
Segmentation fault (core dumped)

What is the reason  ???



I told you to add the -coul flag, not -nocoul.  With the above command,
you're explicitly telling g_enemat to not do anything useful.


-Justin

--
==**==

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin

==**==
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--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Interaction energy..

[rama david]

Hi justin,
I correct command as follow and
 g_enemat -f ener.edr -groups groups.dat -coul -lj

out-put is like


Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 9 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 9 elements, over 50001 frames
Segmentation fault (core dumped)


On Mon, Oct 8, 2012 at 3:22 PM, Justin Lemkul  wrote:

>
>
> On 10/8/12 5:40 AM, rama david wrote:
>
>> Hi justin,
>>
>> As per your advice,
>>
>>   g_enemat -f ener.edr -groups groups.dat -nocoul -nolj
>>
>>
>> Opened ener.edr as single precision energy file
>> Will read groupnames from inputfile
>> Read 2 groups
>> group 0WARNING! could not find group (null):energy-energy (0,0)in energy
>> file
>> WARNING! could not find group (null):energy-extra34 (0,1)in energy file
>> group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
>> file
>>
>> Will select half-matrix of energies with 0 elements
>> Last energy frame read 5 time 1.000
>> Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames
>> Segmentation fault (core dumped)
>>
>> What is the reason  ???
>>
>>
> I told you to add the -coul flag, not -nocoul.  With the above command,
> you're explicitly telling g_enemat to not do anything useful.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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] Interaction energy..

[Justin Lemkul]

On 10/8/12 5:40 AM, rama david wrote:

Hi justin,
As per your advice,

  g_enemat -f ener.edr -groups groups.dat -nocoul -nolj


Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 0 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames
Segmentation fault (core dumped)

What is the reason  ???



I told you to add the -coul flag, not -nocoul.  With the above command, you're 
explicitly telling g_enemat to not do anything useful.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Interaction energy..

[rama david]

Hi justin,
As per your advice,

 g_enemat -f ener.edr -groups groups.dat -nocoul -nolj


Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 0 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames
Segmentation fault (core dumped)

What is the reason  ???

thank you in advance.


With best wishes and regards
Rama david.






On Sat, Oct 6, 2012 at 6:47 PM, Justin Lemkul  wrote:

>
>
> On 10/6/12 6:26 AM, rama david wrote:
>
>> Hi justin,
>>
>> I tried as per your suggestion.
>>
>> command line
>>
>> g_enemat -f ener.edr -groups groups.dat -temp 310  -nolj -free
>>
>> the out put is like ,
>>
>>
>>
>> Opened ener.edr as single precision energy file
>> Will read groupnames from inputfile
>> Read 2 groups
>> group 0WARNING! could not find group (null):energy-energy (0,0)in energy
>> file
>> WARNING! could not find group (null):energy-extra34 (0,1)in energy file
>> group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
>> file
>>
>> Will select half-matrix of energies with 3 elements
>> Last energy frame read 5 time 1.000
>> Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames
>> Segmentation fault (core dumped)
>>
>> why program not work ?? Is it  bug??? or Am I doing any stupid mistake???
>>
>>
> It might be a bug, but I'm not sure yet.  Please run the command without
> the -free option (and thus without -temp) to further reduce complexity.
>  Then manually add the -coul flag.  It should be set by default, but at
> this point the screen output seems to indicate that no energy terms are
> being detected.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
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Re: [gmx-users] Interaction energy..

[Justin Lemkul]

On 10/6/12 6:26 AM, rama david wrote:

Hi justin,

I tried as per your suggestion.

command line

g_enemat -f ener.edr -groups groups.dat -temp 310  -nolj -free

the out put is like ,



Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 3 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames
Segmentation fault (core dumped)

why program not work ?? Is it  bug??? or Am I doing any stupid mistake???



It might be a bug, but I'm not sure yet.  Please run the command without the 
-free option (and thus without -temp) to further reduce complexity.  Then 
manually add the -coul flag.  It should be set by default, but at this point the 
screen output seems to indicate that no energy terms are being detected.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Interaction energy..

[rama david]

Hi justin,

I tried as per your suggestion.

command line

g_enemat -f ener.edr -groups groups.dat -temp 310  -nolj -free

the out put is like ,



Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 3 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames
Segmentation fault (core dumped)

why program not work ?? Is it  bug??? or Am I doing any stupid mistake???

Thank you in advance ..



With best wishes and regards,
Rama david

On Sat, Oct 6, 2012 at 3:40 PM, Justin Lemkul  wrote:

>
>
> On 10/6/12 2:28 AM, rama david wrote:
>
>> Hi justin,
>>
>> the out put of g_energy are like
>>
>> --**--**-
>>1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4
>> LJ-14
>>5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8
>> Disper.-corr.
>>9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
>> Kinetic-En.
>>   13  Total-Energy14  Temperature 15  Pres.-DC16
>> Pressure
>>   17  Constr.-rmsd18  Box-X   19  Box-Y   20
>> Box-Z
>>   21  Volume  22  Density 23  pV  24
>> Enthalpy
>>   25  Vir-XX  26  Vir-XY  27  Vir-XZ  28
>> Vir-YX
>>   29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32
>> Vir-ZY
>>   33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36
>> Pres-XZ
>>   37  Pres-YX 38  Pres-YY 39  Pres-YZ 40
>> Pres-ZX
>>   41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44
>> Box-Vel-XX
>>   45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48
>> Mu-Y
>>   49  Mu-Z50
>> Coul-SR:energy-energy
>>   51  LJ-SR:energy-energy 52
>> LJ-LR:energy-energy
>>   53  Coul-14:energy-energy   54
>> LJ-14:energy-energy
>>   55  Coul-SR:energy-extra34  56
>> LJ-SR:energy-extra34
>>   57  LJ-LR:energy-extra3458
>> Coul-14:energy-extra34
>>   59  LJ-14:energy-extra3460
>> Coul-SR:energy-rest
>>   61  LJ-SR:energy-rest   62
>> LJ-LR:energy-rest
>>   63  Coul-14:energy-rest 64
>> LJ-14:energy-rest
>>   65  Coul-SR:extra34-extra34 66
>> LJ-SR:extra34-extra34
>>   67  LJ-LR:extra34-extra34   68
>> Coul-14:extra34-extra34
>>   69  LJ-14:extra34-extra34   70
>> Coul-SR:extra34-rest
>>   71  LJ-SR:extra34-rest  72
>> LJ-LR:extra34-rest
>>   73  Coul-14:extra34-rest74
>> LJ-14:extra34-rest
>>   75  Coul-SR:rest-rest   76
>> LJ-SR:rest-rest
>>   77  LJ-LR:rest-rest 78
>> Coul-14:rest-rest
>>   79  LJ-14:rest-rest 80
>> T-Protein
>>   81  T-non-Protein   82
>> Lamb-Protein
>>   83  Lamb-non-Protein
>>
>>
>>
>>
>> When I used g_enemat with the groups.dat file like these
>>
>> 2
>> extra34
>> energy
>>
>> I got the output
>>
>>
>> roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy
>> file
>> WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file
>> WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file
>> WARNING! could not find group (null):extra34-energy (0,1)in energy file
>> group 1WARNING! could not find group (null):energy-energy (1,1)in energy
>> file
>>
>> Will select half-matrix of energies with 4 elements
>> Last energy frame read 5 time 1.000
>> Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames
>> Segmentation fault (core dumped)
>>
>>
>> Now When I changed the groups.dat like
>>
>> 2
>> energy
>> extra34
>>
>> ( change in the order of the index groups )
>>
>> I got the following output,
>>
>> Opened ener.edr as single precision energy file
>> Will read groupnames from inputfile
>> Read 2 groups
>> group 0WARNING! could not find group (null):energy-energy (0,0)in energy
>> file
>> WARNING! could not find group (null):energy-extra34 (0,1)in energy file
>> group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
>> file
>>
>> Will select half-matrix of energies with 6 elements
>> Last energy frame read 5 time 1.000
>> Will build energy half-matrix of 2 groups, 6 elements, over 50001 frames
>> Segmentation fault (core dumped)
>>
>>
>>
> Based on the energy names, this is the appropriate setup, but
> unfortunately I have no idea why it does not work.  I have noticed that
> there is a problem with g_enemat - the -lj flag specifies both LJ-SR and
> LJ-LR terms to be written - which may be complicating matters.  Please try
>

Re: [gmx-users] Interaction energy..

[Justin Lemkul]

On 10/6/12 2:28 AM, rama david wrote:

Hi justin,

the out put of g_energy are like

-
   1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4
LJ-14
   5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8
Disper.-corr.
   9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
Kinetic-En.
  13  Total-Energy14  Temperature 15  Pres.-DC16
Pressure
  17  Constr.-rmsd18  Box-X   19  Box-Y   20
Box-Z
  21  Volume  22  Density 23  pV  24
Enthalpy
  25  Vir-XX  26  Vir-XY  27  Vir-XZ  28
Vir-YX
  29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32
Vir-ZY
  33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36
Pres-XZ
  37  Pres-YX 38  Pres-YY 39  Pres-YZ 40
Pres-ZX
  41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44
Box-Vel-XX
  45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48
Mu-Y
  49  Mu-Z50
Coul-SR:energy-energy
  51  LJ-SR:energy-energy 52
LJ-LR:energy-energy
  53  Coul-14:energy-energy   54
LJ-14:energy-energy
  55  Coul-SR:energy-extra34  56
LJ-SR:energy-extra34
  57  LJ-LR:energy-extra3458
Coul-14:energy-extra34
  59  LJ-14:energy-extra3460
Coul-SR:energy-rest
  61  LJ-SR:energy-rest   62
LJ-LR:energy-rest
  63  Coul-14:energy-rest 64
LJ-14:energy-rest
  65  Coul-SR:extra34-extra34 66
LJ-SR:extra34-extra34
  67  LJ-LR:extra34-extra34   68
Coul-14:extra34-extra34
  69  LJ-14:extra34-extra34   70
Coul-SR:extra34-rest
  71  LJ-SR:extra34-rest  72
LJ-LR:extra34-rest
  73  Coul-14:extra34-rest74
LJ-14:extra34-rest
  75  Coul-SR:rest-rest   76
LJ-SR:rest-rest
  77  LJ-LR:rest-rest 78
Coul-14:rest-rest
  79  LJ-14:rest-rest 80
T-Protein
  81  T-non-Protein   82
Lamb-Protein
  83  Lamb-non-Protein




When I used g_enemat with the groups.dat file like these

2
extra34
energy

I got the output


roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy
file
WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file
WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file
WARNING! could not find group (null):extra34-energy (0,1)in energy file
group 1WARNING! could not find group (null):energy-energy (1,1)in energy
file

Will select half-matrix of energies with 4 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames
Segmentation fault (core dumped)


Now When I changed the groups.dat like

2
energy
extra34

( change in the order of the index groups )

I got the following output,

Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 6 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 6 elements, over 50001 frames
Segmentation fault (core dumped)




Based on the energy names, this is the appropriate setup, but unfortunately I 
have no idea why it does not work.  I have noticed that there is a problem with 
g_enemat - the -lj flag specifies both LJ-SR and LJ-LR terms to be written - 
which may be complicating matters.  Please try your command with -nolj to test.





So What is wrong ??
Is I am doing any wrong ??



  2. I am using the temp 310 so the reference temp by default is 300 Should
I have to change it to 310

(-tempreal   300 reference temperature for free energy
calculation )



As stated in the description, the -temp option is for free energy calculations. 
 Are you requesting a free energy calculation?  You haven't provided your 
command line.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Interaction energy..

[rama david]

Hi justin,

the out put of g_energy are like

-
  1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4
LJ-14
  5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8
Disper.-corr.
  9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
Kinetic-En.
 13  Total-Energy14  Temperature 15  Pres.-DC16
Pressure
 17  Constr.-rmsd18  Box-X   19  Box-Y   20
Box-Z
 21  Volume  22  Density 23  pV  24
Enthalpy
 25  Vir-XX  26  Vir-XY  27  Vir-XZ  28
Vir-YX
 29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32
Vir-ZY
 33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36
Pres-XZ
 37  Pres-YX 38  Pres-YY 39  Pres-YZ 40
Pres-ZX
 41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44
Box-Vel-XX
 45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48
Mu-Y
 49  Mu-Z50
Coul-SR:energy-energy
 51  LJ-SR:energy-energy 52
LJ-LR:energy-energy
 53  Coul-14:energy-energy   54
LJ-14:energy-energy
 55  Coul-SR:energy-extra34  56
LJ-SR:energy-extra34
 57  LJ-LR:energy-extra3458
Coul-14:energy-extra34
 59  LJ-14:energy-extra3460
Coul-SR:energy-rest
 61  LJ-SR:energy-rest   62
LJ-LR:energy-rest
 63  Coul-14:energy-rest 64
LJ-14:energy-rest
 65  Coul-SR:extra34-extra34 66
LJ-SR:extra34-extra34
 67  LJ-LR:extra34-extra34   68
Coul-14:extra34-extra34
 69  LJ-14:extra34-extra34   70
Coul-SR:extra34-rest
 71  LJ-SR:extra34-rest  72
LJ-LR:extra34-rest
 73  Coul-14:extra34-rest74
LJ-14:extra34-rest
 75  Coul-SR:rest-rest   76
LJ-SR:rest-rest
 77  LJ-LR:rest-rest 78
Coul-14:rest-rest
 79  LJ-14:rest-rest 80
T-Protein
 81  T-non-Protein   82
Lamb-Protein
 83  Lamb-non-Protein




When I used g_enemat with the groups.dat file like these

2
extra34
energy

I got the output


roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy
file
WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file
WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file
WARNING! could not find group (null):extra34-energy (0,1)in energy file
group 1WARNING! could not find group (null):energy-energy (1,1)in energy
file

Will select half-matrix of energies with 4 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames
Segmentation fault (core dumped)


Now When I changed the groups.dat like

2
energy
extra34

( change in the order of the index groups )

I got the following output,

Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group (null):energy-energy (0,0)in energy
file
WARNING! could not find group (null):energy-extra34 (0,1)in energy file
group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
file

Will select half-matrix of energies with 6 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 6 elements, over 50001 frames
Segmentation fault (core dumped)




So What is wrong ??
Is I am doing any wrong ??



 2. I am using the temp 310 so the reference temp by default is 300 Should
I have to change it to 310

(-tempreal   300 reference temperature for free energy
calculation )

Any suggestion on these topic, is helpful to me.


Thank you in advance,



With best wishes and regards,
Rama david.
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Re: [gmx-users] Interaction energy..

[Justin Lemkul]

On 10/5/12 1:26 PM, rama david wrote:

Hi,
  I got the result by g_energy.
Thank you for these .

but when I used g_enemat with the edr file ( out put from mdrun -rerun )
g_enemat -f ener.edr -groups groups.dat
i got following out put

roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy
file
WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file
WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file
WARNING! could not find group (null):extra34-energy (0,1)in energy file
group 1WARNING! could not find group (null):energy-energy (1,1)in energy
file

Will select half-matrix of energies with 4 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames
Segmentation fault (core dumped)

i used the following groups.dat file

2
extra34
energy


What is reason for the error ?? Is I did any mistake again??



It seems as though the requested energy groups do not exist, though if you have 
obtained quantities through g_energy, this doesn't make much sense.  Can you 
please provide the list of energy terms in the .edr file (from the g_energy 
screen output)?


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Interaction energy..

[rama david]

Hi,
 I got the result by g_energy.
Thank you for these .

but when I used g_enemat with the edr file ( out put from mdrun -rerun )
g_enemat -f ener.edr -groups groups.dat
i got following out put

roup 0WARNING! could not find group (null):extra34-extra34 (0,0)in energy
file
WARNING! could not find group Coul-SR:extra34-energy (0,1)in energy file
WARNING! could not find group LJ-SR:extra34-energy (0,1)in energy file
WARNING! could not find group (null):extra34-energy (0,1)in energy file
group 1WARNING! could not find group (null):energy-energy (1,1)in energy
file

Will select half-matrix of energies with 4 elements
Last energy frame read 5 time 1.000
Will build energy half-matrix of 2 groups, 4 elements, over 50001 frames
Segmentation fault (core dumped)

i used the following groups.dat file

2
extra34
energy


What is reason for the error ?? Is I did any mistake again??

Thank you in advance.


With best wishes and regards,

Rama david


On Fri, Oct 5, 2012 at 10:32 PM, rama david wrote:

> Hi justin,
> Ok now I get
> I have to modify mdp parameter ..
>
> Thank you,
> With best wishes and regards,
> Rama david
>
> On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 10/5/12 11:46 AM, rama david wrote:
>>
>>> Thank you for your Help.
>>>
>>> I did the following tc-groups
>>>
>>> tcoupl= V-rescale; modified Berendsen thermostat
>>> tc-grps=  extra34 Non-Protein energy; two coupling groups -
>>> more accurate
>>> tau_t= 0.10.1 0.1; time constant, in ps
>>> ref_t=  310310 310 ; reference temperature, one for each
>>> group, in K
>>> ;
>>>
>>> Energy contain the residues that i needed
>>> extra34 contain all the remaining ligand and receptor atom
>>> non-protein contain sol and ion.
>>>
>>> I got the energy file after mdrun -rerun
>>>
>>> I used the g_energy term
>>>
>>> It give me the following output
>>> End your selection with an empty line or a zero.
>>> --**--**---
>>>1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4
>>> LJ-14
>>>5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8
>>> Disper.-corr.
>>>9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
>>> Kinetic-En.
>>>   13  Total-Energy14  Temperature 15  Pres.-DC16
>>> Pressure
>>>   17  Constr.-rmsd18  Box-X   19  Box-Y   20
>>> Box-Z
>>>   21  Volume  22  Density 23  pV  24
>>> Enthalpy
>>>   25  Vir-XX  26  Vir-XY  27  Vir-XZ  28
>>> Vir-YX
>>>   29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32
>>> Vir-ZY
>>>   33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36
>>> Pres-XZ
>>>   37  Pres-YX 38  Pres-YY 39  Pres-YZ 40
>>> Pres-ZX
>>>   41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44
>>> Box-Vel-XX
>>>   45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48
>>> Mu-Y
>>>   49  Mu-Z50  T-extra34   51  T-non-Protein   52
>>> T-energy
>>>   53  Lamb-extra3454
>>> Lamb-non-Protein
>>>   55  Lamb-energy
>>>
>>>
>>> So I confused. though it shows the energy group, which option should i
>>> have
>>> to choose ??
>>>
>>> What is Lamb-energy???
>>>
>>>
>> It is related to temperature coupling.
>>
>>
>>  Is I did any mistake??? or I have to use any else command ??
>>>
>>>
>> I have told you to use "energygrps" (which is described in the manual)
>> and you're specifying "tc-grps."  Temperature coupling and energy
>> calculation groups are very different concepts.
>>
>>
>> -Justin
>>
>> --
>> ==**==
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>>
>> ==**==
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>
>
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Re: [gmx-users] Interaction energy..

[rama david]

Hi justin,
Ok now I get
I have to modify mdp parameter ..

Thank you,
With best wishes and regards,
Rama david

On Fri, Oct 5, 2012 at 9:47 PM, Justin Lemkul  wrote:

>
>
> On 10/5/12 11:46 AM, rama david wrote:
>
>> Thank you for your Help.
>>
>> I did the following tc-groups
>>
>> tcoupl= V-rescale; modified Berendsen thermostat
>> tc-grps=  extra34 Non-Protein energy; two coupling groups -
>> more accurate
>> tau_t= 0.10.1 0.1; time constant, in ps
>> ref_t=  310310 310 ; reference temperature, one for each
>> group, in K
>> ;
>>
>> Energy contain the residues that i needed
>> extra34 contain all the remaining ligand and receptor atom
>> non-protein contain sol and ion.
>>
>> I got the energy file after mdrun -rerun
>>
>> I used the g_energy term
>>
>> It give me the following output
>> End your selection with an empty line or a zero.
>> --**--**---
>>1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4
>> LJ-14
>>5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8
>> Disper.-corr.
>>9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
>> Kinetic-En.
>>   13  Total-Energy14  Temperature 15  Pres.-DC16
>> Pressure
>>   17  Constr.-rmsd18  Box-X   19  Box-Y   20
>> Box-Z
>>   21  Volume  22  Density 23  pV  24
>> Enthalpy
>>   25  Vir-XX  26  Vir-XY  27  Vir-XZ  28
>> Vir-YX
>>   29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32
>> Vir-ZY
>>   33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36
>> Pres-XZ
>>   37  Pres-YX 38  Pres-YY 39  Pres-YZ 40
>> Pres-ZX
>>   41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44
>> Box-Vel-XX
>>   45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48
>> Mu-Y
>>   49  Mu-Z50  T-extra34   51  T-non-Protein   52
>> T-energy
>>   53  Lamb-extra3454
>> Lamb-non-Protein
>>   55  Lamb-energy
>>
>>
>> So I confused. though it shows the energy group, which option should i
>> have
>> to choose ??
>>
>> What is Lamb-energy???
>>
>>
> It is related to temperature coupling.
>
>
>  Is I did any mistake??? or I have to use any else command ??
>>
>>
> I have told you to use "energygrps" (which is described in the manual) and
> you're specifying "tc-grps."  Temperature coupling and energy calculation
> groups are very different concepts.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
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Re: [gmx-users] Interaction energy..

[Justin Lemkul]

On 10/5/12 11:46 AM, rama david wrote:

Thank you for your Help.

I did the following tc-groups

tcoupl= V-rescale; modified Berendsen thermostat
tc-grps=  extra34 Non-Protein energy; two coupling groups -
more accurate
tau_t= 0.10.1 0.1; time constant, in ps
ref_t=  310310 310 ; reference temperature, one for each
group, in K
;

Energy contain the residues that i needed
extra34 contain all the remaining ligand and receptor atom
non-protein contain sol and ion.

I got the energy file after mdrun -rerun

I used the g_energy term

It give me the following output
End your selection with an empty line or a zero.
---
   1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4
LJ-14
   5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8
Disper.-corr.
   9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
Kinetic-En.
  13  Total-Energy14  Temperature 15  Pres.-DC16
Pressure
  17  Constr.-rmsd18  Box-X   19  Box-Y   20
Box-Z
  21  Volume  22  Density 23  pV  24
Enthalpy
  25  Vir-XX  26  Vir-XY  27  Vir-XZ  28
Vir-YX
  29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32
Vir-ZY
  33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36
Pres-XZ
  37  Pres-YX 38  Pres-YY 39  Pres-YZ 40
Pres-ZX
  41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44
Box-Vel-XX
  45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48
Mu-Y
  49  Mu-Z50  T-extra34   51  T-non-Protein   52
T-energy
  53  Lamb-extra3454
Lamb-non-Protein
  55  Lamb-energy


So I confused. though it shows the energy group, which option should i have
to choose ??

What is Lamb-energy???



It is related to temperature coupling.


Is I did any mistake??? or I have to use any else command ??



I have told you to use "energygrps" (which is described in the manual) and 
you're specifying "tc-grps."  Temperature coupling and energy calculation groups 
are very different concepts.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Interaction energy..

[rama david]

Thank you for your Help.

I did the following tc-groups

tcoupl= V-rescale; modified Berendsen thermostat
tc-grps=  extra34 Non-Protein energy; two coupling groups -
more accurate
tau_t= 0.10.1 0.1; time constant, in ps
ref_t=  310310 310 ; reference temperature, one for each
group, in K
;

Energy contain the residues that i needed
extra34 contain all the remaining ligand and receptor atom
non-protein contain sol and ion.

I got the energy file after mdrun -rerun

I used the g_energy term

It give me the following output
End your selection with an empty line or a zero.
---
  1  G96Angle 2  Proper-Dih.  3  Improper-Dih.4
LJ-14
  5  Coulomb-14   6  LJ-(SR)  7  LJ-(LR)  8
Disper.-corr.
  9  Coulomb-(SR)10  Coul.-recip.11  Potential   12
Kinetic-En.
 13  Total-Energy14  Temperature 15  Pres.-DC16
Pressure
 17  Constr.-rmsd18  Box-X   19  Box-Y   20
Box-Z
 21  Volume  22  Density 23  pV  24
Enthalpy
 25  Vir-XX  26  Vir-XY  27  Vir-XZ  28
Vir-YX
 29  Vir-YY  30  Vir-YZ  31  Vir-ZX  32
Vir-ZY
 33  Vir-ZZ  34  Pres-XX 35  Pres-XY 36
Pres-XZ
 37  Pres-YX 38  Pres-YY 39  Pres-YZ 40
Pres-ZX
 41  Pres-ZY 42  Pres-ZZ 43  #Surf*SurfTen   44
Box-Vel-XX
 45  Box-Vel-YY  46  Box-Vel-ZZ  47  Mu-X48
Mu-Y
 49  Mu-Z50  T-extra34   51  T-non-Protein   52
T-energy
 53  Lamb-extra3454
Lamb-non-Protein
 55  Lamb-energy


So I confused. though it shows the energy group, which option should i have
to choose ??

What is Lamb-energy???

Is I did any mistake??? or I have to use any else command ??

Thank you in advance

With best wishes and regards.
Rama david.






On Fri, Oct 5, 2012 at 7:54 PM, Justin Lemkul  wrote:

>
>
> On 10/5/12 10:16 AM, rama david wrote:
>
>> Hi gromacs friends,
>>
>> I completed the simulation of receptor and ligand,
>> I visualized the trajectory in the vmd I found  most of the time C
>> terminal
>> (ARG) interact with receptor ( 320 ASP) .
>> I want to find out these interaction energy between these two residues in
>> the simulation.
>>
>>
>>
>> How to find  these interaction energy
>>
>> ( include the LJ and electrostatic interaction)..
>>
>>
> I explained how to do this already.  You need properly set energygrps in
> the .mdp file and an index file that specifies those groups.  The
> quantities you want will then be in the .edr file like all other energy
> terms.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
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Re: [gmx-users] Interaction energy..

[Justin Lemkul]

On 10/5/12 10:16 AM, rama david wrote:

Hi gromacs friends,

I completed the simulation of receptor and ligand,
I visualized the trajectory in the vmd I found  most of the time C terminal
(ARG) interact with receptor ( 320 ASP) .
I want to find out these interaction energy between these two residues in
the simulation.



How to find  these interaction energy

( include the LJ and electrostatic interaction)..



I explained how to do this already.  You need properly set energygrps in the 
.mdp file and an index file that specifies those groups.  The quantities you 
want will then be in the .edr file like all other energy terms.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Interaction energy calculation..

[rama david]

Hi justin,
thank you for reply.

With best wishes and regards
Rama david.



On Fri, Oct 5, 2012 at 4:07 PM, Justin Lemkul  wrote:

>
>
> On 10/5/12 6:15 AM, rama david wrote:
>
>> Hi justin,
>> I completed the simulation ,
>> Now I want to use the selected residues of protein and ligand.
>> How to do it
>>
>> Would you explain me in detail??
>>
>>
> Create a new .tpr file from an .mdp file with suitable energygrps.  Use
> mdrun -rerun to recalculate energies.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Interaction energy calculation..

[Justin Lemkul]

On 10/5/12 6:15 AM, rama david wrote:

Hi justin,
I completed the simulation ,
Now I want to use the selected residues of protein and ligand.
How to do it

Would you explain me in detail??



Create a new .tpr file from an .mdp file with suitable energygrps.  Use mdrun 
-rerun to recalculate energies.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Interaction energy calculation..

[rama david]

Hi justin,
I completed the simulation ,
Now I want to use the selected residues of protein and ligand.
How to do it

Would you explain me in detail??

With best wishes and regards,
Rama david.


On Fri, Oct 5, 2012 at 3:40 PM, Justin Lemkul  wrote:

>
>
> On 10/5/12 5:49 AM, rama david wrote:
>
>> Hi Friends,
>>
>> I want to study the interaction energy between the selected residues of
>> protein and ligand.
>>
>> ( Non-bonded energy should include : vanderwall and electrostatics)
>>
>> How to do it???
>>
>>
> This is what the energygrps keyword in the .mdp file is for.  Beware the
> interpretation and utility of these quantities.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Interaction energy calculation..

[Justin Lemkul]

On 10/5/12 5:49 AM, rama david wrote:

Hi Friends,

I want to study the interaction energy between the selected residues of
protein and ligand.

( Non-bonded energy should include : vanderwall and electrostatics)

How to do it???



This is what the energygrps keyword in the .mdp file is for.  Beware the 
interpretation and utility of these quantities.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] Interaction energy

[Justin A. Lemkul]

Steven Neumann wrote:



On Tue, Oct 18, 2011 at 11:41 AM, Justin A. Lemkul > wrote:




Steven Neumann wrote:



On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Steven Neumann wrote:

   Dear Gmx Users,
I would like to calculate the interaction energy (LJ and
   electrostatic) between each residue and my ligands (10
ligands
   in the system). I would like to see what is the
contribution of
   electrostatic and vdW interactions between ligand and
each of my
   residue. I thought to use g_energy and specify each of my
   residues in index files but it is not possible. Will you
suggest
   how to do this?
   


   For such information, you have to specify these groups as
energygrps
   in the .mdp file.  You can rerun the trajectory using mdrun
-rerun
   and a new .tpr file specifying these groups, but depending on the
   output frequency, the result may not be as accurate as you'd
like.

   -Justin

 Thank you Justin. Now I have two groups sepcified in my mdp file:
 energygrps = Protein LIG

How can I specify each residue of my protein separately and each
ligand? In my md.gro file I have residues:

   91GLY 92TYR . 161LIG 162LIG...

 Will it be correct like this
 energygrps = 91GLY 92 TYR ... 161LIG 162LIG...
 



No.  The names must correspond to valid groups in an index file.

 
So do you mean that that I should add my index file with
 


grompp -f md.mdp -c npt.gro -n *index.ndx* -t npt.cpt -p topol.top -o md.tpr

 

with specified groups in md.mdp file like they are specified in index 
file? :) Then just to


 


mdrun -rerun -deffnm md2

 


Please, let me know whether I am correct or not.



Yes.

-Justin

 


Steven


If yes, will this simulation take longer? Thank you


Perhaps, but certainly your energy file will be considerably larger.

-Justin

 Steven

 
 



-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080

http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


==__==
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--


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


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Re: [gmx-users] Interaction energy

[Steven Neumann]

On Tue, Oct 18, 2011 at 11:41 AM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>
>>
>> On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Steven Neumann wrote:
>>
>>Dear Gmx Users,
>> I would like to calculate the interaction energy (LJ and
>>electrostatic) between each residue and my ligands (10 ligands
>>in the system). I would like to see what is the contribution of
>>electrostatic and vdW interactions between ligand and each of my
>>residue. I thought to use g_energy and specify each of my
>>residues in index files but it is not possible. Will you suggest
>>how to do this?
>>
>>
>>For such information, you have to specify these groups as energygrps
>>in the .mdp file.  You can rerun the trajectory using mdrun -rerun
>>and a new .tpr file specifying these groups, but depending on the
>>output frequency, the result may not be as accurate as you'd like.
>>
>>-Justin
>>
>>  Thank you Justin. Now I have two groups sepcified in my mdp file:
>>  energygrps = Protein LIG
>>
>> How can I specify each residue of my protein separately and each ligand?
>> In my md.gro file I have residues:
>>
>>91GLY 92TYR . 161LIG 162LIG...
>>
>>  Will it be correct like this
>>  energygrps = 91GLY 92 TYR ... 161LIG 162LIG...
>>
>>
>
> No.  The names must correspond to valid groups in an index file.
>
>
So do you mean that that I should add my index file with


grompp -f md.mdp -c npt.gro -n *index.ndx* -t npt.cpt -p topol.top -o md.tpr



with specified groups in md.mdp file like they are specified in index file?
:) Then just to



mdrun -rerun -deffnm md2



Please, let me know whether I am correct or not.



Steven

>
> If yes, will this simulation take longer? Thank you
>>
>
> Perhaps, but certainly your energy file will be considerably larger.
>
> -Justin
>
>  Steven
>>
>>
>>
>>
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
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Re: [gmx-users] Interaction energy

[Justin A. Lemkul]

Steven Neumann wrote:



On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul > wrote:




Steven Neumann wrote:

Dear Gmx Users,
 I would like to calculate the interaction energy (LJ and
electrostatic) between each residue and my ligands (10 ligands
in the system). I would like to see what is the contribution of
electrostatic and vdW interactions between ligand and each of my
residue. I thought to use g_energy and specify each of my
residues in index files but it is not possible. Will you suggest
how to do this?
 



For such information, you have to specify these groups as energygrps
in the .mdp file.  You can rerun the trajectory using mdrun -rerun
and a new .tpr file specifying these groups, but depending on the
output frequency, the result may not be as accurate as you'd like.

-Justin

 
Thank you Justin. Now I have two groups sepcified in my mdp file:
 
energygrps = Protein LIG


How can I specify each residue of my protein separately and each ligand? 
In my md.gro file I have residues:


91GLY 92TYR . 161LIG 162LIG...

 
Will it be correct like this
 
energygrps = 91GLY 92 TYR ... 161LIG 162LIG...
 


No.  The names must correspond to valid groups in an index file.


If yes, will this simulation take longer? Thank you


Perhaps, but certainly your energy file will be considerably larger.

-Justin

 
Steven


 

 



--


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] Interaction energy

[Steven Neumann]

On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>> Dear Gmx Users,
>>  I would like to calculate the interaction energy (LJ and electrostatic)
>> between each residue and my ligands (10 ligands in the system). I would like
>> to see what is the contribution of electrostatic and vdW interactions
>> between ligand and each of my residue. I thought to use g_energy and specify
>> each of my residues in index files but it is not possible. Will you suggest
>> how to do this?
>>
>>
>
> For such information, you have to specify these groups as energygrps in the
> .mdp file.  You can rerun the trajectory using mdrun -rerun and a new .tpr
> file specifying these groups, but depending on the output frequency, the
> result may not be as accurate as you'd like.
>
> -Justin
>
>
Thank you Justin. Now I have two groups sepcified in my mdp file:

energygrps = Protein LIG

How can I specify each residue of my protein separately and each ligand? In
my md.gro file I have residues:

> 91GLY 92TYR . 161LIG 162LIG...


Will it be correct like this

energygrps = 91GLY 92 TYR ... 161LIG 162LIG...

If yes, will this simulation take longer? Thank you

Steven
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Re: [gmx-users] Interaction energy

[Justin A. Lemkul]

Steven Neumann wrote:

Dear Gmx Users,
 
I would like to calculate the interaction energy (LJ and 
electrostatic) between each residue and my ligands (10 ligands in the 
system). I would like to see what is the contribution of electrostatic 
and vdW interactions between ligand and each of my residue. I thought to 
use g_energy and specify each of my residues in index files but it is 
not possible. Will you suggest how to do this?
 


For such information, you have to specify these groups as energygrps in the .mdp 
file.  You can rerun the trajectory using mdrun -rerun and a new .tpr file 
specifying these groups, but depending on the output frequency, the result may 
not be as accurate as you'd like.


-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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Please search the archive at 
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[gmx-users] Interaction energy

[Steven Neumann]

Dear Gmx Users,

I would like to calculate the interaction energy (LJ and
electrostatic) between each residue and my ligands (10 ligands in the
system). I would like to see what is the contribution of electrostatic and
vdW interactions between ligand and each of my residue. I thought to use
g_energy and specify each of my residues in index files but it is not
possible. Will you suggest how to do this?

Thank you,

Steven
-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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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 pos

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
> > 
> 
> -- 
> =

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 
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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.
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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


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[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 ! 



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[gmx-users] Interaction energy

[ANINDITA GAYEN]

Dear all, 
   
I have simulated a small peptide (+2 charge at pH=7) in water. Then i
calculate the interaction energy using "energy_grps = Protein
SOL". The value of different energy terms are as
follows:
Coul-SR:SOL_CL--Protein: -1290
(KJ/mol)
LJ-SR:SOL_CL--Protein:    -157
(KJ/mol)
LJ-LR:SOL_CL--Protein: -13
(KJ/mol)
Are these values are reasonable?

Thanks in advance.

Anindita




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Re: [gmx-users] interaction energy

[Justin A. Lemkul]

On 1/10/10 7:40 AM, leila karami wrote:

Hi
I want to obtain interaction energy between protein and dna in
simulation pr-dna complex.
what command is suitable for that?


Please read about energygrps in the manual.

-Justin



Any help will highly appreciated!



--


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] interaction energy

[leila karami]

Hi

I want to obtain interaction energy between protein and dna in simulation
pr-dna complex.

what command is suitable for that?


Any help will highly appreciated!
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Re: [gmx-users] interaction energy of bulk TIP3P

[Mark Abraham]

sandeep somani wrote:
i see. i reran the trajectory with reaction field electrostatics and 
that gave a more negative energy value which was closer to what i was 
expecting.


i guess the missing reciprocal space contributions explains this 
discrepancy.


is there a way to get the full interaction energy with PME ?


I've never heard of a groupwise decomposition of the reciprocal space 
sum. For a single component system, there might to be some cunning way 
of deducing it from the total energy.


Mark
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Re: [gmx-users] interaction energy of bulk TIP3P

[sandeep somani]

i see. i reran the trajectory with reaction field electrostatics and that
gave a more negative energy value which was closer to what i was expecting.

i guess the missing reciprocal space contributions explains this
discrepancy.

is there a way to get the full interaction energy with PME ?

thnx for the reply
-sandeep



On Nov 17, 2007 8:18 PM, Mark Abraham <[EMAIL PROTECTED]> wrote:

> > Hi All
> >
> > I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and
> PME
> > for 400 ps and extracted the interaction energy of a randomly picked
> water
> > molecule with rest of the system.
> > Simulation was done at 298K and 1bar and usual procedure for generating
> a
> > water box and equilibration were used.
> >
> > Average interaction energy reported in the log file was
> > Epot (kJ/mol)Coul-SR  LJ-SR
> >   WAT-rest   -8.13828e+011.21886e+01
> >
> > giving a total of  -8.13828e+01  + 1.21886e+01 = -69.194 kJ/mol
> >
> > Comparing with published numbers using other MD programs this should be
> in
> > the range of -81 +/- 1 kJ/mol i.e. ~11 kJ/mol less.
> >
> > any clues on origin of this discrepancy ?  relevant .top , .mdp files
> are
> > below.
>
> The PME algorithm does an approximation to the full periodic Coulomb
> summation, but does so with a calculation in direct space, as above, and
> another in reciprocal space, where your energy groups are not meaningful.
> So you're only getting the direct-space component of the interaction
> energy.
>
> Mark
>
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Re: [gmx-users] interaction energy of bulk TIP3P

[Mark Abraham]

> Hi All
>
> I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and PME
> for 400 ps and extracted the interaction energy of a randomly picked
water
> molecule with rest of the system.
> Simulation was done at 298K and 1bar and usual procedure for generating
a
> water box and equilibration were used.
>
> Average interaction energy reported in the log file was
> Epot (kJ/mol)Coul-SR  LJ-SR
>   WAT-rest   -8.13828e+011.21886e+01
>
> giving a total of  -8.13828e+01  + 1.21886e+01 = -69.194 kJ/mol
>
> Comparing with published numbers using other MD programs this should be
in
> the range of -81 +/- 1 kJ/mol i.e. ~11 kJ/mol less.
>
> any clues on origin of this discrepancy ?  relevant .top , .mdp files
are
> below.

The PME algorithm does an approximation to the full periodic Coulomb
summation, but does so with a calculation in direct space, as above, and
another in reciprocal space, where your energy groups are not meaningful.
So you're only getting the direct-space component of the interaction
energy.

Mark

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[gmx-users] interaction energy of bulk TIP3P

[sandeep somani]

Hi All

I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and PME
for 400 ps and extracted the interaction energy of a randomly picked water
molecule with rest of the system.
Simulation was done at 298K and 1bar and usual procedure for generating a
water box and equilibration were used.

Average interaction energy reported in the log file was
Epot (kJ/mol)Coul-SR  LJ-SR
  WAT-rest   -8.13828e+011.21886e+01

giving a total of  -8.13828e+01  + 1.21886e+01 = -69.194 kJ/mol

Comparing with published numbers using other MD programs this should be in
the range of -81 +/- 1 kJ/mol i.e. ~11 kJ/mol less.

any clues on origin of this discrepancy ?  relevant .top , .mdp files are
below.

Thanks
Sandeep


;---
*;MD.MDP for bulk TIP3P *
;---
cpp =  /usr/bin/cpp
constraints =  all-bonds
integrator  =  md
tinit   =  0.0
dt  =  0.002
nsteps  =  20 ; 400  ps
nstcomm =  1
nstxout =  50
nstlog  =  50
nstenergy   =  50
nstxtcout   =  50
nstlist =  5
energygrps  =  WAT
ns_type =  grid
;PME
coulombtype =  PME
rlist   =  0.9
rcoulomb=  0.9
rvdw=  0.9
fourierspacing  =  0.12
pme_order   =  4
ewald_rtol  =  1e-5
optimize_fft=  yes
; Temperature coupling
Tcoupl  =  berendsen
tc-grps =   SOL WAT
tau_t   =   0.1 0.1
ref_t   =  298  298
; Pressure coupling is on
Pcoupl  =  berendsen
Pcoupltype  =  isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
;---
*; TOP FILE FOR TIP3P BULK *
; Include forcefield parameters
#include "ffoplsaa.itp"
; Include water topology
#include "tip3p.itp"
[ system ]
; Name
bulk water
[ molecules ]
; Compound#mols
SOL 2180
--

*bits of log file from production run:*

   <==  ###  ==>
   <  A V E R A G E S  >
   <==  ###  ==>

  Energies (kJ/mol)
   LJ (SR)   Coulomb (SR)   Coul. recip.  PotentialKinetic En.
   1.35174e+04   -8.91571e+04   -1.10392e+04   -8.66790e+041.61998e+04
  Total EnergyTemperature Pressure (bar)
  -7.04792e+042.97985e+022.27514e+00

 Box-X  Box-Y  Box-Z Volume   Density (SI)
   4.06327e+004.06327e+004.06327e+006.70858e+019.72133e+02
pV
   9.03527e+00

  Total Virial (kJ/mol)
   5.40366e+03   -6.97436e+002.78681e+00
  -6.97436e+005.38940e+03   -2.37439e+00
   2.78681e+00   -2.37439e+005.39318e+03

  Pressure (bar)
  -2.28378e+003.27978e+00   -1.13390e+00
   3.27978e+004.65423e+001.52221e+00
  -1.13390e+001.52221e+004.45496e+00

  Total Dipole (Debye)
   3.23351e+00   -1.12569e+011.42062e+01

 Epot (kJ/mol)Coul-SR  LJ-SR
   WAT-WAT0.0e+000.0e+00
  WAT-rest   -8.13828e+011.21886e+01
 rest-rest   -8.90758e+041.35052e+04

 T-SOL  T-WAT
   2.97985e+022.97422e+02


   M E G A - F L O P S   A C C O U N T I N G

  RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
  T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
  NF=No Forces

Computing:M-Number M-Flops  % of Flops
---
Coul(T) + LJ [W3-W3]  21419.733112  8182338.04878466.4
Outer nonbonded loop   3168.78223231687.822320 0.3
Spread Q Bspline  83712.418560   167424.837120 1.4
Gather F Bspline  83712.418560  1004549.022720 8.2
3D-FFT   263902.919508  2111223.35606417.1
Solve PME  4287.521437   274401.372000 2.2
NS-Pairs  10955.692493   230069.542353 1.9
Reset In Box261.606540 2354.458860 0.0
Shift-X2616.01308015696.078480 0.1
CG-CoM   87.202180 2528.863220 0.0
Virial 1313.40656723641.318206 0.2
Update 1308.00654040548.202740 0.3
Stop-CM1308.0013080.00 0.1
P-Coupling 1308.006540 7848.039240 0.1
Calc-Ekin  1308.01308035316.353160 0.3
Constraint-V   1308.006540 7848.039240 0.1
Constraint-Vir 1308.01962031392.470880 0.3
Settle  436.006540   140830.112420 1.1
---
Total  12322777.937807   100.0
---

Re: [gmx-users] interaction energy between the ligand and protein

[Mark Abraham]

Rui Li wrote:

Hello!

 Can I estimate the inhibit capability by interaction energy between the ligand
and protein?


Only about as well as you can estimate the results of a Formula One 
racing season from the marks the drivers got on their drivers license exams.



And how can I get the interaction energy in Gromacs?


Energy groups. See the manual.

Mark
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[gmx-users] interaction energy between the ligand and protein

[Rui Li]

Hello!

 Can I estimate the inhibit capability by interaction energy between the ligand
and protein? And how can I get the interaction energy in Gromacs?


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[gmx-users] Interaction energy calculation in a radius

[aloks]

Hi all,
I want to calculate interaction energy between my ligand and residues of
proetins which come within 6A of any atoms of the raidus. I have defined
those residues and ligand as different groups. But how to select water
around 6A radius of the ligand during dynamicsfor the calculation. If I
consider all the water atoms for my calculation, huge contribution by
water molecules, i guess is giving lots of background and so I am getting
+ve values!

Any suggestion would be highly appreciated

alok
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