[gmx-users] problem with topology
ml.perrotta at itm.cnr.it
Tue Jun 11 13:29:10 CEST 2019
Thank you for your rapid answer.
1- No I haven't an itp for each molecule. I wrote opls atomtypes on n2t
files that is in oplsaa.ff directory.
2- To generate the box with the two kind of molecules I used the gmx
insert-molecules command. Ar first I inserted 100 molecules of PVDF and
then the 1436 molecules of ATBC, setting box size at 15x15x15nm (x,y and
z). Then I wanted a smaller box size (in particular 10.2x10.2x10.2) and so
I used the command gmx editconf , in particular
gmx editconf -f oldbox.gro -o newbox.gro -box 10.2 10.2 10.2 -density 1000
It because I want a density of the system equal to 1 g/ml. I think that
the problem is in this stage, because if I compare the oldbox.gro and the
newbox.gro trough using of VMD I see differents bond from molecules, and I
think that they interact.So in this case the system is not able to
recognize these bonds.
Anyway the exact command that I used to create topology is:
gmx x2top -f newbox.gro -o topol.top -ff oplsaa
> Do you have a .itp for each molecule? How did you generate the box with
> multiple molecules? What is the contents of your .top file? What was the
> exact commands you used? What was the exact output? Copy and paste, do not
> type out what you think it says.
> Suspect there may be a problem with how you are calling the topology.
> On Tue, 11 Jun. 2019, 6:32 pm Maria Luisa, <ml.perrotta at itm.cnr.it> wrote:
>> Dear user.
>> I have a problem. I have to simulate a box of 100 molecules of
>> polyvinylidene fluoride (PVDF) and 1436 molecules of the solvent ATBC.
>> first I built the single chain of PVDf and a single molecules of ATBC,
>> I was able to construct topology using opls force-field. The command
>> I used is gmx x2top. When I create the complete box with a total amount
>> 95320 atoms, an error occurs saying to me that it's possible recognize
>> only 1800 atoms of 95320. This is strange, because the two molecules are
>> written in the topology file each one, but not together in the box. What
>> is the problem? Is there some bug with my version of gromacs (5.1.4)?
>> I wait for your answer
>> Maria Luisa
>> Maria Luisa Perrotta
>> Ph.D Student, CNR-ITM
>> via P.Bucci, 87036 Rende (Cs)
>> email: ml.perrotta at itm.cnr.it
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Maria Luisa Perrotta
Ph.D Student, CNR-ITM
via P.Bucci, 87036 Rende (Cs)
email: ml.perrotta at itm.cnr.it
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