tinkertools / tinker-openmm Goto Github PK

Dear All,

I'm trying to install the tinker-openmm interface on Ubuntu 20.04. I have followed the installation instructions without facing any problems, until the step "(6) Run the "make" command to build executables. When the build is finished, there will be three executables produced in the build directory, "analyze_omm.x", "bar_omm.x" and "dynamic_omm.x". "

The make command gives the following error:

gfortran -c -Ofast -msse3 -fopenmp ommdata.f -o ommdata.o
ommdata.f:100:44:

100 | & ybox2,zbox2,box23,volbox,alpha_sin,alpha_cos,
| 1
Error: Symbol ‘box23’ at (1) has no IMPLICIT type; did you mean ‘box34’?
make: *** [Makefile:730: ommdata.o] Error 1

My gfortran, gcc, and g++ versions are 9.4.0. The installed OpenMM version is 7.5.0. I am also using the CUDA v11.4, if this is relevant.

Could anyone help me navigate this problem?

Thank you all.

I was trying to build tinker-openmm interface but I am getting the following error (please refer to the image uploaded)

ERROR:
After typing the command "make all", is shows the error,
ommstuf.cpp(2991): error: identifier "OpenMM_AmoebaVdwForce_addParticle_1" is undefined
OpenMM_AmoebaVdwForce_addParticle_1 (amoebaVdwForce, vdw__.ired[ii]-1, cdnstype, vdw__.kred[ii], isAlchemical);
Can someone please help me in resolving this problem?

Hi,

I would like to follow the force components on each atom during the molecular dynamics run (AMOEBA in Tinker-OpenMM). However, the keyword "save-force" appends the same values in each dynamics step. I observe this issue only using GPU via OpenMM interface. Could you please advise me how to get the forces in each step properly?

Thanks in advance!

Hi there!

I’m trying to build Tinker-OpenMM from source and i’m encountering the following error message on stage 6 after running $make all, as specified in the invocation options contained in ’Makefile’.

g++ -c -Ofast -msse3 -fopenmp -I/usr/local/openmm/include ommstuf.cpp
ommstuf.cpp:57:10: fatal error: OpenMMCWrapper.h: No such file or directory
#include "OpenMMCWrapper.h"
^~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [ommstuf.o] Error 1

As for a bit of extra context, I’m in an anaconda environment containing OpenMM 7.5 which I installed using:

$conda install -c conda-forge openmm=7.5.0

How should I proceed?

Many thanks,
Max