Hi
I am trying to alter a topology to include 3 virtual sites and I have a
few queries, the answers to which are not obvious form the manual.
Do I declare the virtual sites in the atomtypes directive like so
;type mass charge ptype sigma(nm)
epsilon(kjmol-1)
CB
Hi
Having tried to run grompp using the data below I keep getting the
following error
Fatal error:
Unknown vsiten type 7
Does anyone know why this might be?
Gavin
Gavin Melaugh wrote:
Hi
I am trying to alter a topology to include 3 virtual sites and I have a
few queries, the answers to which
Gavin Melaugh wrote:
Hi
Having tried to run grompp using the data below I keep getting the
following error
Fatal error:
Unknown vsiten type 7
Does anyone know why this might be?
Your [virtual_sites] directive is not correct, either in its name (no such thing
as virtual_sitesn - the n
Hi Justin
Thanks for the reply. To create a virtual site at the centre of geometry
of 3 atoms, according to the manual, do you not say: [virtual_sitesn],
the index of the site, the index of the three atoms and then the
function type 1 which determines that it is COG.
Or as I now realise. State
Gavin Melaugh wrote:
Hi Justin
Thanks for the reply. To create a virtual site at the centre of geometry
of 3 atoms, according to the manual, do you not say: [virtual_sitesn],
the index of the site, the index of the three atoms and then the
function type 1 which determines that it is COG.
Justin
I have tried this but I am now getting different errors. I take it that:
I specify the virtual sites in the atomtypes directive as I have seen
from examples?
I index the virtual sites in the atoms directive in accordance with the
rest of the molecule. atom numbers go from 1-228, therefore
Gavin Melaugh wrote:
Justin
I have tried this but I am now getting different errors. I take it that:
I specify the virtual sites in the atomtypes directive as I have seen
from examples?
Virtual sites are included in all the force fields already, but if you want some
custom name, then yes,
Yeah I see your point about the types. With regard to the initial
configuration state I would have assumed that gromacs knew the initial
position of the virtual site when I stated that it was to be at the
COG of the 3 atoms in the [virtual_sitesn] directive.
Justin A. Lemkul wrote:
Gavin
Gavin Melaugh wrote:
Yeah I see your point about the types. With regard to the initial
configuration state I would have assumed that gromacs knew the initial
position of the virtual site when I stated that it was to be at the
COG of the 3 atoms in the [virtual_sitesn] directive.
I
O.k Cheers
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Yeah I see your point about the types. With regard to the initial
configuration state I would have assumed that gromacs knew the initial
position of the virtual site when I stated that it was to be at the
COG of the 3 atoms in the
On 6/05/2011 10:17 PM, Gavin Melaugh wrote:
Yeah I see your point about the types. With regard to the initial
configuration state I would have assumed that gromacs knew the initial
position of the virtual site when I stated that it was to be at the
COG of the 3 atoms in the [virtual_sitesn]
Hi Mark
Cheers.Could you perhaps shed some insight into format of
[virtual_siten] when trying to define the VS at the COG of three atoms.
It is not obvious from the manual
Cheers
Gavin
Mark Abraham wrote:
On 6/05/2011 10:17 PM, Gavin Melaugh wrote:
Yeah I see your point about the types. With
On 6/05/2011 10:39 PM, Gavin Melaugh wrote:
Hi Mark
Cheers.Could you perhaps shed some insight into format of
[virtual_siten] when trying to define the VS at the COG of three atoms.
It is not obvious from the manual
Indeed, it's undocumented - but I think Sikander's experience from my
Mark Abraham wrote:
On 6/05/2011 10:39 PM, Gavin Melaugh wrote:
Hi Mark
Cheers.Could you perhaps shed some insight into format of
[virtual_siten] when trying to define the VS at the COG of three atoms.
It is not obvious from the manual
Indeed, it's undocumented - but I think Sikander's
Hi Mark
Many thanks to you and all your colleagues for replying. This has
worked, at least there are now no errors. Where the manual is incorrect
is that it leads you to believe that you state;
[virtual _siten]
;index of VS index of atoms for COG func
229 8 11 15
Am I correct in saying now, from the following topology (exerpts), that
the virtual site VS will only interact with C3?
I guess I don't have to give the atom indices of this interaction in the
pair list which I use only for 1_4 interactions?
Can I use sigma and epsilon in the nonbond_params
Yes, since sigma and epsilon are zero for VS then interactions between and
VS-VS and VS-(any other atom) would result in zero force. Since you
explicitly define the interaction between VS-C3, combination rule won't be
used and C6(VS_C3) and C12(VS_C3) will be computed as per sigma(VS_C3)
Cheers Sikandar
I take it that because combination rule 3 (provide sigma and epsilon) is
stated gromacs assumes that all values in nonbonding parameters are
sigma and epsilon. I know this tp be tru for the atomtypes but does it
filter down to all intermolecular interactions.
Cheers
Gavin
yes it will...
On Fri, May 6, 2011 at 11:02 AM, Gavin Melaugh gmelaug...@qub.ac.uk wrote:
Cheers Sikandar
I take it that because combination rule 3 (provide sigma and epsilon) is
stated gromacs assumes that all values in nonbonding parameters are
sigma and epsilon. I know this tp be tru for
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