Thank you for your response.
The column "Order of parameters and their units" of table 5.5 states that I have to include a value for n and the force constant k.
I tried it by simply setting k to 1:
[ bonds ]
;ai aj func n k
1 2 9 0 1
;ai aj func n k
1 2 9 0 1
it produces a similar error message (now for the angles instead of the bonds):
Fatal error:
Incorrect number of parameters - found 1, expected 2 or 4 for Tab. Angles.
Incorrect number of parameters - found 1, expected 2 or 4 for Tab. Angles.
(I also added the n and k in the [angles] part like:
[ angles ]
; ai aj ak angleTyp n k
1 2 3 8 1 1
; ai aj ak angleTyp n k
1 2 3 8 1 1
because of the fact that table 5.5 also states that I have to include a value for n and the force constant k for the angles.
)
Any idea if I have to secify further values? (Some which are not in table 5.5)
Or does anybody know the activator for such an error message?
Thank you in advance!
Best,
Liz
Gesendet: Dienstag, 04. August 2015 um 15:33 Uhr
Von: "Mark Abraham" <mark.j.abra...@gmail.com>
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] tabulated bonded interaction functions
Von: "Mark Abraham" <mark.j.abra...@gmail.com>
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] tabulated bonded interaction functions
Hi,
Yes you have to specify k. That detail is in table 5.5, to which that
section refers you.
Mark
On Tue, Aug 4, 2015 at 3:26 PM Liz Bell <lizb...@gmx.at> wrote:
> Dear all,
> Regarding my question concerning the format of the [bonds] part of the topology file, I tried some new things:
> Changing the [bonds] part in the topology to:
> [ bonds ]
> ;ai aj func n
> 1 2 9 0
>
> for n=0 (and therefore the file: table_b0.xvg) produces this error
> message:
>
> Fatal error:
> Incorrect number of parameters - found 1, expected 2 or 4 for Tab. Bonds.
>
> But the other error message reported in the first post vanished.
> I would be really grateful if somebody could tell me how the line in the
> [bonds] part has to look like when using tabulated boned interactions.
> Do I for example have to specify the force constant reported in the 4.2.14
> section of the manual (by simply writing it behind the n) ?
>
> Best,
> Liz
>
>
> *Gesendet:* Dienstag, 04. August 2015 um 14:41 Uhr
> *Von:* "Liz Bell" <lizb...@gmx.at>
> *An:* gromacs.org_gmx-users@maillist.sys.kth.se
> *Betreff:* [gmx-users] tabulated bonded interaction functions
>
> Dear all,
>
> I am perfoming MD simulations of P3Ht chains and I would like to define the bonded as well as the nonbonded parameters using tables.
> Regarding the bonded parameters, there are no problems until now, as I simply wrote some additional lines in the mdp file (similar to this explanation: http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials).
> But how do I tell gromacs to use the information for [bonds], [angles]... (all the bonded potentials)... from table_b0.xvg for example.
>
> The first line of the [bonds] section in my topology file looks like:
> [ bonds ]
> ;ai aj func
> 1 2 9
> Where 1 and 2 are the atoms and 9 is the function type.
> Running grompp produces various of those mistakes:
>
> No default Tab. Bonds NC types
> No default Lin. Angle types
> No default Proper Dih. types
>
> I think Gromacs can not find the values that I defined in the
> table_b*.xvg, table_a*.xvg and table_d*.xvg.
>
> The section 4.2.12 in the gromacs manual tells "...for a bond with n=0 [...] the table is read from the file table_b0.xvg.
> But where do I have to specify that the atoms 1 2 have the bonds with n=0, with the information provided in the table_b0.xvg?
>
> Does anybody know how to adapt the topology file, or whether some
> additional lines are needed in the mdp files?
>
> Thank you very much in advance,
>
> Liz
> -- Gromacs Users mailing list * Please search the archive at
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Yes you have to specify k. That detail is in table 5.5, to which that
section refers you.
Mark
On Tue, Aug 4, 2015 at 3:26 PM Liz Bell <lizb...@gmx.at> wrote:
> Dear all,
> Regarding my question concerning the format of the [bonds] part of the topology file, I tried some new things:
> Changing the [bonds] part in the topology to:
> [ bonds ]
> ;ai aj func n
> 1 2 9 0
>
> for n=0 (and therefore the file: table_b0.xvg) produces this error
> message:
>
> Fatal error:
> Incorrect number of parameters - found 1, expected 2 or 4 for Tab. Bonds.
>
> But the other error message reported in the first post vanished.
> I would be really grateful if somebody could tell me how the line in the
> [bonds] part has to look like when using tabulated boned interactions.
> Do I for example have to specify the force constant reported in the 4.2.14
> section of the manual (by simply writing it behind the n) ?
>
> Best,
> Liz
>
>
> *Gesendet:* Dienstag, 04. August 2015 um 14:41 Uhr
> *Von:* "Liz Bell" <lizb...@gmx.at>
> *An:* gromacs.org_gmx-users@maillist.sys.kth.se
> *Betreff:* [gmx-users] tabulated bonded interaction functions
>
> Dear all,
>
> I am perfoming MD simulations of P3Ht chains and I would like to define the bonded as well as the nonbonded parameters using tables.
> Regarding the bonded parameters, there are no problems until now, as I simply wrote some additional lines in the mdp file (similar to this explanation: http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials).
> But how do I tell gromacs to use the information for [bonds], [angles]... (all the bonded potentials)... from table_b0.xvg for example.
>
> The first line of the [bonds] section in my topology file looks like:
> [ bonds ]
> ;ai aj func
> 1 2 9
> Where 1 and 2 are the atoms and 9 is the function type.
> Running grompp produces various of those mistakes:
>
> No default Tab. Bonds NC types
> No default Lin. Angle types
> No default Proper Dih. types
>
> I think Gromacs can not find the values that I defined in the
> table_b*.xvg, table_a*.xvg and table_d*.xvg.
>
> The section 4.2.12 in the gromacs manual tells "...for a bond with n=0 [...] the table is read from the file table_b0.xvg.
> But where do I have to specify that the atoms 1 2 have the bonds with n=0, with the information provided in the table_b0.xvg?
>
> Does anybody know how to adapt the topology file, or whether some
> additional lines are needed in the mdp files?
>
> Thank you very much in advance,
>
> Liz
> -- Gromacs Users mailing list * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
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