[gmx-users] Re: Positive potential energy for TFE solvent

[Harpreet Basra]

hi,

I am still stuck with same problem of obtaining positive potential energy.

>>On 11/11/2011 5:07 PM, Harpreet Basra wrote:
>> Hi
>>
>> I am trying to generate an equilibrated box of 216 TFE molecules.To
>> generate the 216 TFE molecule box i performed following steps:
>
>A suggested workflow can be found here
>http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation

I have been following this link only.

>
>
>> 1) I got the tfe.gro file and created a cubic box of edge length =
>> 0.516 nm containing 1 TFE molecule (at its center), using the
>> following command:
>>
 editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516
>>  I chose this length because in the tfe.gro file dimensions of the TFE
>> molecule are 0.516 0.516 0.516.
>
>That's not a good reason. Choose a volume and shape that makes sense for
>your target density. Cubic probably doesn't make sense when a
>rectangular shape is possible. Then you'll probably want to choose -nbox
>differently later.

I chose a rectangular box too. still i get a positive value for PE and
moreover all the molecules move towards two opposite walls of the box. I am
not sure that the way I am using the genconf command is the correct way.
because I have tried every other possibility for not getting a positive
potential, with no success. So here are my .gro file and the topology file
for TFE.

 the energy of this one molecule (tfe.gro) was coming out to b e highly
negative (-6.4E+08 kJ/mol). But on generating a solvent system with 216
molecules the energy becomes (1.9E+04 kJ/mol).

**tfe.gro file*

 7
1TFE   F1T   1   0.444   0.344   0.246
1TFE   CT 2   0.334  0.245   0.246
1TFE   F2T3   0.350  0.160   0.364
1TFE   F3T4   0.350  0.160   0.127
1TFE   CH2T  5  0.187  0.326   0.246
1TFE   OT  6  0.075  0.220   0.246
1TFE   HT  7  -0.019 0.266   0.246
0.49174   0.49174   0.49174

topology file
[ moleculetype ]
; Name nrexcl
TFE 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 FTFE1  TFE  F1T   1   -0.170   18.9984
2 CTFE1  TFE  CT10.452   12.0110
3 FTFE1  TFE  F2T   1   -0.170   18.9984
4 FTFE1  TFE  F3T   1   -0.170   18.9984
5 CHTFE 1  TFE  CH2T 10.273   14.0270
6 OTFE   1  TFE  OT 1   -0.625   15.9994
7 H  1  TFE  HT 1   0.410   1.0080
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1
2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2
2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3
2 5 2 0.153 715.0 0.153 715.0 ; C1 C2
5 6 2 0.143 818.0 0.143 818.0 ; C2 O
6 7 2 0.100 1570.0 0.100 1570.0 ; O H
[ pairs ]
; ai aj fu c0, c1, ...
1 6 1 ; F1 O
2 7 1 ; C1 H
3 6 1 ; F2 O
4 6 1 ; F3 O
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2
1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3
1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2
3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3
3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2
4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2
2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O
5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1
2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H

To construct a box of TFE solvent i took the tfe.gro file and replicated
the TFE molecule by using


genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6


can u plz suggest is it that I am using genconf in a wrong way that it is
causing this problem? I am not sure how many molecules (-nbox option in
genconf) should i keep in the box in order to get a mass density of 1383g/L
for TFE. Though i checked the denity of solvent box i constructed the
average valu comes out to be 1397g/L with a std deviation of 30g/L. thus
it seems range.

thanks

Harpreet

>
>> 2) Then using genconf command i replicated the box to get a bigger box
>> with 216 TFE molecules using the following command:
>>
 genconf -f tfe_box.gro  -o out.gro -rot -nbox 6
>> 3) Energy minimization was done using STEEPEST descent
>>
>> 4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns
>> NPT (300K, 1atm) equilibration.
>>
>> After doing all these steps still I obtain a positive a potentail
>> energy. I get positive potential energy of the system (2.45+E04
>> kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive
>> total energy of the system. My question is whether obtaining positive
>> potential energy indicate some error in my TFE solvent box ? Is it
>> because of large Fluorine atoms of TFE ? Does it mean its not properly
>> equilibrated ? What can I do to equilibrate it?
>
>You probably have atomic overlaps from your choice of cubic 0.516 box
>earlier. Did you look at the results of genconf before computing with them?
>
>Mark
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[gmx-users] Re: Positive potential energy for TFE solvent

[Harpreet Basra]

Hi Mark,

Thanks for the quick reply. But i have already done what u suggested.


>
> On 15/11/2011 6:06 PM, Harpreet Basra wrote:
> > Hi
> > I am still stuck with same problem of obtaining positive potential
> > energy.
> > >>On 11/11/2011 5:07 PM, Harpreet Basra wrote:
> > >> Hi
> > >>
> > >> I am trying to generate an equilibrated box of 216 TFE molecules.To
> > >> generate the 216 TFE molecule box i performed following steps:
> > >
> > >A suggested workflow can be found here
> > >http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation
> > I have been following this link only.
> > >
> > >
> > >> 1) I got the tfe.gro file and created a cubic box of edge length =
> > >> 0.516 nm containing 1 TFE molecule (at its center), using the
> > >> following command:
> > >>
> >  editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516
> > >>  I chose this length because in the tfe.gro file dimensions of the TFE
> > >> molecule are 0.516 0.516 0.516.
> > >
> > >That's not a good reason. Choose a volume and shape that makes sense for
> > >your target density. Cubic probably doesn't make sense when a
> > >rectangular shape is possible. Then you'll probably want to choose -nbox
> > >differently later.
> > I chose a rectangular box too. still i get a positive value for PE and
> > moreover all the molecules move towards two opposite walls of the box.
> > I am not sure that the way I am using the genconf command is the
> > correct way. because I have tried every other possibility for not
> > getting a positive potential, with no success. So here are my .gro
> > file and the topology file for TFE.
> > *tfe.gro file*
> > 7
> >
> > 1TFE   F1T   1   0.444   0.344   0.246
> >
> > 1TFE   CT 2   0.334  0.245   0.246
> >
> > 1TFE   F2T3   0.350  0.160   0.364
> >
> > 1TFE   F3T4   0.350  0.160   0.127
> >
> > 1TFE   CH2T  5  0.187  0.326   0.246
> >
> > 1TFE   OT  6  0.075  0.220   0.246
> >
> > 1TFE   HT  7  -0.019 0.266   0.246
> >
> > 0.49174   0.49174   0.49174
> >
> > topology file
> >
> > [ moleculetype ]
> >
> > ; Name nrexcl
> >
> > TFE 3
> >
> > [ atoms ]
> >
> > ; nr type resnr resid atom cgnr charge mass
> >
> > 1 FTFE1  TFE  F1T   1   -0.170   18.9984
> >
> > 2 CTFE1  TFE  CT10.452   12.0110
> >
> > 3 FTFE1  TFE  F2T   1   -0.170   18.9984
> >
> > 4 FTFE1  TFE  F3T   1   -0.170   18.9984
> >
> > 5 CHTFE 1  TFE  CH2T 10.273   14.0270
> >
> > 6 OTFE   1  TFE  OT 1   -0.625   15.9994
> >
> > 7 H  1  TFE  HT 1   0.410   1.0080
> >
> > [ bonds ]
> >
> > ; ai aj fu c0, c1, ...
> >
> > 2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1
> >
> > 2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2
> >
> > 2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3
> >
> > 2 5 2 0.153 715.0 0.153 715.0 ; C1 C2
> >
> > 5 6 2 0.143 818.0 0.143 818.0 ; C2 O
> >
> > 6 7 2 0.100 1570.0 0.100 1570.0 ; O H
> >
> > [ pairs ]
> >
> > ; ai aj fu c0, c1, ...
> >
> > 1 6 1 ; F1 O
> >
> > 2 7 1 ; C1 H
> >
> > 3 6 1 ; F2 O
> >
> > 4 6 1 ; F3 O
> >
> > [ angles ]
> >
> > ; ai aj ak fu c0, c1, ...
> >
> > 1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2
> >
> > 1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3
> >
> > 1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2
> >
> > 3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3
> >
> > 3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2
> >
> > 4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2
> >
> > 2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O
> >
> > 5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H
> >
> > [ dihedrals ]
> >
> > ; ai aj ak al fu c0, c1, m, ...
> >
> > 6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1
> >
> > 2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H
> >
> > and to construct a box of TFE solvent i took the tfe.gro file and
> > replicated the TFE molecule by using
> > genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6
> > can u plz suggest is it that I am using genconf in a wrong way that it
> > is causing this problem? I am not sure how many molecules (-nbox
> > option in genconf) should i keep in the box in order to get a mass
> > density of 1383g/L for TFE.
>
> That link says "Work out how much volume a single molecule would have in
> the box of your chosen density and size. Useeditconf
> to place a box of that size around your
> single molecule." It does not seem to me that you have done this.
>
> Mark
>

I did place the *single molecule* in a box of size required to get a
density of 1383 g/L. I also checked the density of the solvent box
(containing 216 molecules after NVT equilibration for 200 ps) I constructed
the average value comes out to be 1397 g/L with a std deviation of 30 g/L,
thus it seems range. Moreover, the potential energy of this one molecule
(tfe.gro) was coming out to be highly negative (-6.4E+08 kJ/mol). But on
generating a solvent system with 216 TFE molecules the energy becomes
(1.9E+04 kJ/mol).

Harpreet
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/

Re: [gmx-users] Re: Positive potential energy for TFE solvent

[Mark Abraham]

On 16/11/2011 1:18 AM, Harpreet Basra wrote:

Hi Mark,

Thanks for the quick reply. But i have already done what u suggested.



On 15/11/2011 6:06 PM, Harpreet Basra wrote:
> Hi
> I am still stuck with same problem of obtaining positive potential
> energy.
> >>On 11/11/2011 5:07 PM, Harpreet Basra wrote:
> >> Hi
> >>
> >> I am trying to generate an equilibrated box of 216 TFE
molecules.To
> >> generate the 216 TFE molecule box i performed following steps:
> >
> >A suggested workflow can be found here
> >http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation
> I have been following this link only.
> >
> >
> >> 1) I got the tfe.gro file and created a cubic box of edge
length =
> >> 0.516 nm containing 1 TFE molecule (at its center), using the
> >> following command:
> >>
>  editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516
> >>  I chose this length because in the tfe.gro file dimensions
of the TFE
> >> molecule are 0.516 0.516 0.516.
> >
> >That's not a good reason. Choose a volume and shape that makes
sense for
> >your target density. Cubic probably doesn't make sense when a
> >rectangular shape is possible. Then you'll probably want to
choose -nbox
> >differently later.
> I chose a rectangular box too. still i get a positive value for
PE and
> moreover all the molecules move towards two opposite walls of
the box.
> I am not sure that the way I am using the genconf command is the
> correct way. because I have tried every other possibility for not
> getting a positive potential, with no success. So here are my .gro
> file and the topology file for TFE.
> *tfe.gro file*
> 7
>
> 1TFE   F1T   1   0.444   0.344   0.246
>
> 1TFE   CT 2   0.334  0.245   0.246
>
> 1TFE   F2T3   0.350  0.160   0.364
>
> 1TFE   F3T4   0.350  0.160   0.127
>
> 1TFE   CH2T  5  0.187  0.326   0.246
>
> 1TFE   OT  6  0.075  0.220   0.246
>
> 1TFE   HT  7  -0.019 0.266   0.246
>
> 0.49174   0.49174   0.49174
>
> topology file
>
> [ moleculetype ]
>
> ; Name nrexcl
>
> TFE 3
>
> [ atoms ]
>
> ; nr type resnr resid atom cgnr charge mass
>
> 1 FTFE1  TFE  F1T   1   -0.170   18.9984
>
> 2 CTFE1  TFE  CT10.452   12.0110
>
> 3 FTFE1  TFE  F2T   1   -0.170   18.9984
>
> 4 FTFE1  TFE  F3T   1   -0.170   18.9984
>
> 5 CHTFE 1  TFE  CH2T 10.273   14.0270
>
> 6 OTFE   1  TFE  OT 1   -0.625   15.9994
>
> 7 H  1  TFE  HT 1   0.410   1.0080
>
> [ bonds ]
>
> ; ai aj fu c0, c1, ...
>
> 2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1
>
> 2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2
>
> 2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3
>
> 2 5 2 0.153 715.0 0.153 715.0 ; C1 C2
>
> 5 6 2 0.143 818.0 0.143 818.0 ; C2 O
>
> 6 7 2 0.100 1570.0 0.100 1570.0 ; O H
>
> [ pairs ]
>
> ; ai aj fu c0, c1, ...
>
> 1 6 1 ; F1 O
>
> 2 7 1 ; C1 H
>
> 3 6 1 ; F2 O
>
> 4 6 1 ; F3 O
>
> [ angles ]
>
> ; ai aj ak fu c0, c1, ...
>
> 1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2
>
> 1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3
>
> 1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2
>
> 3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3
>
> 3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2
>
> 4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2
>
> 2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O
>
> 5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H
>
> [ dihedrals ]
>
> ; ai aj ak al fu c0, c1, m, ...
>
> 6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1
>
> 2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H
>
> and to construct a box of TFE solvent i took the tfe.gro file and
> replicated the TFE molecule by using
> genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6
> can u plz suggest is it that I am using genconf in a wrong way
that it
> is causing this problem? I am not sure how many molecules (-nbox
> option in genconf) should i keep in the box in order to get a mass
> density of 1383g/L for TFE.

That link says "Work out how much volume a single molecule would
have in
the box of your chosen density and size. Useeditconf
to place a box of that size
around your
single molecule." It does not seem to me that you have done this.

Mark


I did place the *single molecule* in a box of size required to get a 
density of 1383 g/L. I also checked the density of the solvent box 
(containing 216 molecules after NVT equilibration for 200 ps) I 
constructed the average value comes ou