Re: [gmx-users] Query

[Mark Abraham]

On 4/23/2011 4:54 PM, NAGA MANI wrote:

editconf -f conf.gro -o newbox.gro -c -d 1.0 -bt dodecahedron

while typing this command i got error...

Fatal error: Atom type CH3 not found...


I think you were using a different command when you saw this error. If 
you copy and paste more of the context when reporting an error, you will 
make it much easier for someone to help you. See 
http://www.gromacs.org/Documentation/Errors


Mark



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Re: [gmx-users] How to control the temperature when using an electric field?

[Apoorv Kalyankar]

In GROMACS, I believe that whenever an external force is applied, the
mean velocity of the group is subtracted before rescaling the
velocities and then the mean velocity is added back in. So if you are
expecting  a plug like flow then there should not be any problem. In
other cases also, it should not create a problem since your external
electric field is not that large.

And yes you should not remove the center of mass motion of the
molecules otherwise you will get zero velocity.

Apoorv

On Fri, Apr 22, 2011 at 2:09 AM, lammps lammps  wrote:
> Hi,
>
> I want to use the option of E_x = 1   0.01  0 to add an electric field to
> the simulated system in NVT ensemble.
>
> Because there should exist an no zero velocity of center-of-mass in the x
> direction. It seems that it is wrong to directly use the nose-hoover to
> control the temperature.
>
> it is also not reasonable to use nstcomm   = 1, because the velocity of
> center-of mass in the x-axis should be kept when runing.
>
> So, How to control the temperature? When calcating the temperature in the
> process of simulations, how to exclude the velocity of center-of-mass of x
> direction for controling the right T?
>
> Thanks in advance.
>
> --
> wade
>
> --
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Re: [gmx-users] How to control the temperature when using an electric field?

[David van der Spoel]

On 2011-04-23 09.38, Apoorv Kalyankar wrote:

In GROMACS, I believe that whenever an external force is applied, the
mean velocity of the group is subtracted before rescaling the
velocities and then the mean velocity is added back in. So if you are
expecting  a plug like flow then there should not be any problem. In
other cases also, it should not create a problem since your external
electric field is not that large.

This is correct for the acceleration option, but not for the electric 
field. Hence the E-field will introduce friction that will heat up the 
system.



And yes you should not remove the center of mass motion of the
molecules otherwise you will get zero velocity.

Correct.


Apoorv

On Fri, Apr 22, 2011 at 2:09 AM, lammps lammps  wrote:

Hi,

I want to use the option of E_x = 1   0.01  0 to add an electric field to
the simulated system in NVT ensemble.

Because there should exist an no zero velocity of center-of-mass in the x
direction. It seems that it is wrong to directly use the nose-hoover to
control the temperature.

it is also not reasonable to use nstcomm   = 1, because the velocity of
center-of mass in the x-axis should be kept when runing.

So, How to control the temperature? When calcating the temperature in the
process of simulations, how to exclude the velocity of center-of-mass of x
direction for controling the right T?

Thanks in advance.

--
wade

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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] How to control the temperature when using an electric field?

[lammps lammps]

Thank Apoorv and David,

If the GMX can use the volecities of y-axis and z-axis, it will
overcome this question.

However, it seems that the question was not resolved on the basis of David.

Any other people give some advice?

Thanks very much.

2011/4/23 David van der Spoel 

> On 2011-04-23 09.38, Apoorv Kalyankar wrote:
>
>> In GROMACS, I believe that whenever an external force is applied, the
>> mean velocity of the group is subtracted before rescaling the
>> velocities and then the mean velocity is added back in. So if you are
>> expecting  a plug like flow then there should not be any problem. In
>> other cases also, it should not create a problem since your external
>> electric field is not that large.
>>
>> This is correct for the acceleration option, but not for the electric
> field. Hence the E-field will introduce friction that will heat up the
> system.
>
>
> And yes you should not remove the center of mass motion of the
>> molecules otherwise you will get zero velocity.
>>
> Correct.
>
>
>> Apoorv
>>
>> On Fri, Apr 22, 2011 at 2:09 AM, lammps lammps
>>  wrote:
>>
>>> Hi,
>>>
>>> I want to use the option of E_x = 1   0.01  0 to add an electric field to
>>> the simulated system in NVT ensemble.
>>>
>>> Because there should exist an no zero velocity of center-of-mass in the x
>>> direction. It seems that it is wrong to directly use the nose-hoover to
>>> control the temperature.
>>>
>>> it is also not reasonable to use nstcomm   = 1, because the velocity of
>>> center-of mass in the x-axis should be kept when runing.
>>>
>>> So, How to control the temperature? When calcating the temperature in the
>>> process of simulations, how to exclude the velocity of center-of-mass of
>>> x
>>> direction for controling the right T?
>>>
>>> Thanks in advance.
>>>
>>> --
>>> wade
>>>
>>> --
>>> 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!
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>>>
>>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] dealing with ATP

[Sajad Ahrari]

Dear users
i am working with a protein witch holds a hetero-atom in it's pdb structure. 
the 
hetero-atom  is named "d" and stands for "ADP+SO4" (in fact the third phosphate 
of ATP is being substituted with SO4). i wanted to know if gromacs holds a 
feature to change "d" into ATP? and if so do i need to introduce ATP for 
Gromacs 
or it is known for the program?
i do appreciate your help!
sajad
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Re: [gmx-users] dealing with ATP

[Justin A. Lemkul]

Sajad Ahrari wrote:

Dear users
i am working with a protein witch holds a hetero-atom in it's pdb 
structure. the hetero-atom  is named "d" and stands for "ADP+SO4" (in 
fact the third phosphate of ATP is being substituted with SO4). i wanted 
to know if gromacs holds a feature to change "d" into ATP? and if so do 


No, but you can use a text editor to replace the S atom with P.


i need to introduce ATP for Gromacs or it is known for the program?


Some force fields support ATP, some do not.  Check the .rtp files and see what 
you find.


-Justin


i do appreciate your help!
sajad



--


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] dealing with ATP

[Sajad Ahrari]

tnx for your help Justin!
but shouldn't the topology of S atom be described for gromacs? unless gromacs 
may know P atom with the same topology as S. although they may not be the same!?
regards
sajad





From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Sat, April 23, 2011 5:54:58 AM
Subject: Re: [gmx-users] dealing with ATP



Sajad Ahrari wrote:
> Dear users
> i am working with a protein witch holds a hetero-atom in it's pdb structure. 
>the hetero-atom  is named "d" and stands for "ADP+SO4" (in fact the third 
>phosphate of ATP is being substituted with SO4). i wanted to know if gromacs 
>holds a feature to change "d" into ATP? and if so do 
>

No, but you can use a text editor to replace the S atom with P.

> i need to introduce ATP for Gromacs or it is known for the program?

Some force fields support ATP, some do not.  Check the .rtp files and see what 
you find.

-Justin

> i do appreciate your help!
> sajad
> 

-- 

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] dealing with ATP

[Justin A. Lemkul]

Sajad Ahrari wrote:

tnx for your help Justin!
but shouldn't the topology of S atom be described for gromacs? unless 
gromacs may know P atom with the same topology as S. although they may 
not be the same!?


You're talking about two separate issues - atom types and parameters for 
molecules.  Yes, most (all?) force fields describe both P and S atoms, but I 
guarantee none of them have (by default) parameters for some species named "d" 
that represents ADP-SO4.  You cannot assign parameters from P blindly to S and 
hope for the best.  That sounds fundamentally wrong to me.


In your original message, it sounded like you wanted to change ADP-SO4 into ATP, 
but perhaps I misunderstood what you intended.  No force field will be able to 
assign parameters to ADP-SO4, even though the force field may recognize 
individual atoms, it cannot construct a topology for any arbitrary molecules.


If you need to simulation this ADP-SO4 species, you're in for the long road of 
parameterization:


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

Otherwise, change the S atom to P and name the molecule ATP so it will be 
recognized by whatever force field you choose, after you have verified that the 
force field can indeed recognize such a species.  Otherwise, you're stuck doing 
parameterization for ATP, too.


-Justin


regards
sajad


*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Sat, April 23, 2011 5:54:58 AM
*Subject:* Re: [gmx-users] dealing with ATP



Sajad Ahrari wrote:
 > Dear users
 > i am working with a protein witch holds a hetero-atom in it's pdb 
structure. the hetero-atom  is named "d" and stands for "ADP+SO4" (in 
fact the third phosphate of ATP is being substituted with SO4). i wanted 
to know if gromacs holds a feature to change "d" into ATP? and if so do


No, but you can use a text editor to replace the S atom with P.

 > i need to introduce ATP for Gromacs or it is known for the program?

Some force fields support ATP, some do not.  Check the .rtp files and 
see what you find.


-Justin

 > i do appreciate your help!
 > sajad
 >

-- 

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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[gmx-users] Re: Cylinder Pulling output file pullx.xvg wrong

[Kun Huang]

Dear Chris:

Thanks for you reply. You are right. The printf in gromacs 4.0.7 is very
different from gromacs 4.5.3. and the output file in gromacs 4.5.3 is right.
I think they fixed the bug :)

Thank you very much,
Kun

On Mon, Apr 18, 2011 at 1:41 PM,  wrote:

> Send gmx-users mailing list submissions to
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> Today's Topics:
>
>   1. Re: Re: energy group exclusions (Justin A. Lemkul)
>   2. Re: diverging temperature with pressure coupling (Dommert Florian)
>   3. Cylinder Pulling output file pullx.xvg wron
>  (chris.ne...@utoronto.ca)
>   4. Simulation of CNT with Amber forcefield (majid hasan)
>   5. Re: Simulation of CNT with Amber forcefield (Justin A. Lemkul)
>   6. protein-ligand complex tutorial (ahmet y?ld?r?m)
>
>
> --
>
> Message: 1
> Date: Mon, 18 Apr 2011 07:27:27 -0400
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] Re: energy group exclusions
> To: Discussion list for GROMACS users 
> Message-ID: <4dac201f.2010...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Sikandar Mashayak wrote:
> > Also, what about non-bonded interactions within the protein? Does
> > exclusion group only exclude the non-bonded interactions between two
> > different molecules and non-bonded interactions within the single
> > molecule atoms are still computed?
> >
>
> Nonbonded interactions are excluded between each defined pair.  Therefore,
> with
>
> energygrp_excl = Protein Protein SOL SOL
>
> you are excluding all nonbonded interactions between protein atoms (Protein
> Protein pair) and between solvent atoms (SOL SOL pair).  Protein-solvent
> interactions are calculated.  The use of energygrp_excl (as documented)
> indicates that only nonbonded interactions are affected.  That is, bonded
> energies should still be calculated for all groups.
>
> -Justin
>
> > On Sun, Apr 17, 2011 at 10:38 PM, Sikandar Mashayak
> > mailto:symasha...@gmail.com>> wrote:
> >
> > Hi
> >
> > When we define energy group exclusions e.g. like in manual energygrp
> > excl = Protein Protein SOL SOL
> > and do md rerun, then only non-bonded interactions between Protein
> > and SOL are computed. I am wondering what happens to bonded
> > interactions within the protein, do they contribute to energies even
> > though we have excluded protein-protein interactions?
> >
> > thanks
> > sikandar
> >
> >
>
> --
> 
>
> 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
>
> 
>
>
> --
>
> Message: 2
> Date: Mon, 18 Apr 2011 13:41:42 +0200
> From: Dommert Florian 
> Subject: Re: [gmx-users] diverging temperature with pressure coupling
> To: Discussion list for GROMACS users 
> Message-ID: <1303126902.2464.107.camel@fermi>
> Content-Type: text/plain; charset="utf-8"
>
> On Mon, 2011-04-18 at 11:42 +0200, David van der Spoel wrote:
> > On 2011-04-18 11.22, Dommert Florian wrote:
> > > Hello,
> > >
> > > oh this nasty ILs ;) I am currently investigating a similar problem,
> > > that deals with PR-coupling and my impression is that Leap-Frog is the
> > > problem and not PR. Currently I am running simulations with md-vv and
> > > MTTK to verify my ideas. On the other hand I am using two tc_groups for
> > > my ILs due their difference in size. Unfortunately you have not written
> > > which IL you deal with, but thinking about long chain ILs like
> > > [BMIM][Cl], or [BMIM][PF6], the degrees of freedom for the different
> > > molecules differ strongly. Here the big question is why does the
> > > barostat influence the thermostat. It seems one has to be very very
> > > careful, when choosing the coupling parameter for PR. I did a bunch of
> > > simulations just varying the coupling parameter and obtained large
> > > differences in the dynamics of my system, while static properties like
> > > RDF, density of mass, and pressure look quite fine. For example if I
> > > calculate the conductivity including correlation effects the values
> > > differ from 2 S/m up to 12 S/m. But so far I also have no idea why ???
> > > I am really happy when I finally got my results with vv and if you are
> > > interested I can report back to the list or off-list, just let me know.
> > >
> > > On the o

[gmx-users] Potential energy methanol in a box

[Fabian Casteblanco]

Hello,

I'm trying to fill a box with methanol using CHARMM FF Parameters.  I
also need to do this for ethanol and 1-propanol.

For ethanol, each individual molecule had approximately -19 kJ/mol of
potential energy, then I placed 1000 in a box, performed nvt, npt,
etc.  End Result:  A negative potential energy (it means that its
stable?)  and a density of 0.785 g/cm3 compared to actual 0.789 g/cm3
at 1 atm, 298 K.  This result seemed ok.

For methanol and  1-propanol, each individual molecule had a larger
24 - 64 kJ/mol respectively, due to Coulomb 1,4 pair interactions (for
example, for methanol between the HA 0.09 and the H 0.43 gives a large
64 kJ/mol).  Again placed 1000 each in 2 separate boxes, performed
nvt,npt,etc on each one.  End Result:  A still positive potential
energy for each box (shouldn't this be negative after running npt? on
both) and a density that was 0.789 g/cm3 (for 1-propanol)compared to
actual 0.803 g/cm3 1-propanol at 1 atm, 298 K.  Methanol density a bit
closer 0.787 compared to 0.791 g/cm3.

My questions are:
-There should definetly be a positive potential energy after running
npt, correct? Otherwise it wouldn't be stable?  I understand that the
1,4 coulomb interactions should cancel out with nearby molecules.
*For CHARMM, they state that unless otherwise 1,4 parameters exist
already, they use a full scale 1.0 of the regular LJ, coulomb
potential.

-As for the density, I know it's somewhat close but I'm trying to be
as accurate as possible.  I read somewhere that the average cut-off
(rlist) is usually 1.4 for CHARMM and I had mine set to 1.  I'm
guessing that having a larger cutoff would contribute more molecules
to the LJ, coulomb which might rise the density a bit to the correct
value?

I'm still new to Gromacs so I appreciate all of anybodys help.  Thanks a bunch.

--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com


minim.mdp
Description: Binary data


nvt.mdp
Description: Binary data


npt.mdp
Description: Binary data


ethanol.itp
Description: Binary data


methanol.itp
Description: Binary data


1propanol.itp
Description: Binary data
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Re: [gmx-users] Potential energy methanol in a box

[Justin A. Lemkul]

Fabian Casteblanco wrote:

Hello,

I'm trying to fill a box with methanol using CHARMM FF Parameters.  I
also need to do this for ethanol and 1-propanol.

For ethanol, each individual molecule had approximately -19 kJ/mol of
potential energy, then I placed 1000 in a box, performed nvt, npt,
etc.  End Result:  A negative potential energy (it means that its
stable?)  and a density of 0.785 g/cm3 compared to actual 0.789 g/cm3
at 1 atm, 298 K.  This result seemed ok.



Negative potential implies net attraction.  Positive potential implies net 
repulsion.  Systems in the condensed phase typically have negative potential 
energies, but you should not necessarily equate negative energy with stability. 
 Unstable systems can have negative potential, too.  But if your trajectory 
itself is stable, then likely so too is the system you're looking at.



For methanol and  1-propanol, each individual molecule had a larger
24 - 64 kJ/mol respectively, due to Coulomb 1,4 pair interactions (for
example, for methanol between the HA 0.09 and the H 0.43 gives a large
64 kJ/mol).  Again placed 1000 each in 2 separate boxes, performed
nvt,npt,etc on each one.  End Result:  A still positive potential
energy for each box (shouldn't this be negative after running npt? on
both) and a density that was 0.789 g/cm3 (for 1-propanol)compared to
actual 0.803 g/cm3 1-propanol at 1 atm, 298 K.  Methanol density a bit
closer 0.787 compared to 0.791 g/cm3.


Negative potential does not simply arise from NPT simulation.  The potential is 
determined by the topology and functional form used.  Something about these 
systems is causing a net repulsion, and it may very well be the intramolecular 
interactions.  That seems likely, since the densities you're getting are 
slightly low, indicating that the molecules are insufficiently condensed.




My questions are:
-There should definetly be a positive potential energy after running
npt, correct? Otherwise it wouldn't be stable?  I understand that the


No.  See above.  Ensemble does not dictate whether or not the potential is 
positive or negative.  The topology does.



1,4 coulomb interactions should cancel out with nearby molecules.


No.  1-4 interactions are intramolecular.  They are not dependent upon the 
presence or absence of nearby molecules.  They are dependent upon the 
configurations of the individual molecules themselves.



*For CHARMM, they state that unless otherwise 1,4 parameters exist
already, they use a full scale 1.0 of the regular LJ, coulomb
potential.



Correct.


-As for the density, I know it's somewhat close but I'm trying to be
as accurate as possible.  I read somewhere that the average cut-off
(rlist) is usually 1.4 for CHARMM and I had mine set to 1.  I'm
guessing that having a larger cutoff would contribute more molecules
to the LJ, coulomb which might rise the density a bit to the correct
value?



The value of the cutoff should be no less than 1.2-1.4 nm, according to the 
CHARMM developers (http://dx.doi.org/10.1002/jcc.21287).  It's hard to predict 
the effects of such changes, since they will affect neighbor searching, balance 
of PME terms, and others.  You should certainly be using settings recommended 
(and used) by the force field developers, unless you have a substantive reason 
not to (i.e., someone has developed better settings).


-Justin


I'm still new to Gromacs so I appreciate all of anybodys help.  Thanks a bunch.

--
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.castebla...@gmail.com



--


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_hbond in 4.5.4 gives wrong output

[Bert]

Dear all,

g_hbond of gromacs4.0.7 and 4.5.4 gives different outputs in average
hbond number. Is there any fix to g_hbond of 4.5.4? Any suggestions
are appreciated.

Bests,
Bert
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Re: [gmx-users] g_hbond in 4.5.4 gives wrong output

[Justin A. Lemkul]

Bert wrote:

Dear all,

g_hbond of gromacs4.0.7 and 4.5.4 gives different outputs in average
hbond number. Is there any fix to g_hbond of 4.5.4? Any suggestions
are appreciated.



This is a known bug and is present (as far as I know) in all 4.5.x versions. 
There is no fix yet.


-Justin


Bests,
Bert


--


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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