Hi Justin,
Thanks, I just posted redmine issue #3204.
Will try pull code.
On Thu, Nov 14, 2019 at 6:02 AM Justin Lemkul wrote:
>
>
> On 11/12/19 6:30 PM, Dave M wrote:
> > Hi Justin,
> >
> > I am having troubles now with domain decompositions when I use openMPI
> > mpirun but it works fine
On 11/12/19 6:30 PM, Dave M wrote:
Hi Justin,
I am having troubles now with domain decompositions when I use openMPI
mpirun but it works fine when I run on single mpi. My system is quite large
(80x80x80) and I defined additional bonds in top file as:
[ intermolecular_interactions ]
[
Hi Justin,
I am having troubles now with domain decompositions when I use openMPI
mpirun but it works fine when I run on single mpi. My system is quite large
(80x80x80) and I defined additional bonds in top file as:
[ intermolecular_interactions ]
[ bonds ]
; ai aj type
3123 40767 6
On 11/10/19 4:53 AM, Dave M wrote:
Hi Justin,
I just found that using bond type 6 (instead of 1) works for my test
models. So something like this in top file works fine which is bit neat and
easier to handle for multiple molecules (compared to pull code).
[intermolecular_interactions]
[
Hi Justin,
I just found that using bond type 6 (instead of 1) works for my test
models. So something like this in top file works fine which is bit neat and
easier to handle for multiple molecules (compared to pull code).
[intermolecular_interactions]
[ bonds ]
1 158 6 0.4 1000
On 11/5/19 7:53 PM, Dave M wrote:
Hi Justin,
Will appreciate any suggestions about the error am getting with
distance_restraints.
Aside from using the pull code rather than this approach, I have no
other suggestions.
-Justin
Thanks.
regards,
Dave
On Thu, Oct 31, 2019 at 1:39 AM Dave
Hi Justin,
Will appreciate any suggestions about the error am getting with
distance_restraints.
Thanks.
regards,
Dave
On Thu, Oct 31, 2019 at 1:39 AM Dave M wrote:
> Hi Justin,
>
> Thanks, not sure [distance_restraints] also does not work for me. Though
> pull code works (like shared by other
Hi Justin,
Thanks, not sure [distance_restraints] also does not work for me. Though
pull code works (like shared by other user Mustafa in recent discussions).
My top files contain this:
[ intermolecular_interactions ]
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
1 155
On 10/28/19 6:21 PM, Dave M wrote:
Hi Justin,
Thanks for your reply but am getting error suggesting a intermolecular
chemical bond is not allowed:
Program: gmx grompp, version 2016.4
Source file: src/gromacs/gmxpreprocess/convparm.cpp (line 649)
Fatal error:
The
Hi Justin,
Thanks for your reply but am getting error suggesting a intermolecular
chemical bond is not allowed:
Program: gmx grompp, version 2016.4
Source file: src/gromacs/gmxpreprocess/convparm.cpp (line 649)
Fatal error:
The intermolecular_interaction can not contain chemically bonding
On 10/27/19 9:24 PM, Dave M wrote:
Hi All,
I am trying to define a bond between two molecules. Their parameters are
defined in separate itp files: molA.itp and molB.itp. I know I can
combine both the itp files but I am just wondering if I can define extra
bonds/angles joining two molecules
Dave,
What you are looking to achieve might be doable using the the .rpt file
(entry for each molecule), specbond.dat (into which you put the special
bond) then run your coordinate file through pdb2gmx, making the entire
topology which will also now include the intermolecular bond.
On Mon, 28
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