Merge pull request #127 from Becksteinlab/no-append

- remove -append from GROMACS run options
- user reports in #126 that this PR fixed issue

CHANGES

@@ -5,20 +5,25 @@ CHANGES for MDPOW
 Add summary of changes for each release. Use ISO dates. Reference
 GitHub issues numbers and PR numbers.
 
-2019-xx-xx    0.7.0
+2021-xx-xx    0.7.0
 orbeckst, VOD555
 
- * renamed package to MDPOW
- * removed all generated docs from package
- * config parser MERGES user runinput.yml with the package defaults
-   (#8)
- * boxtype and minimum distance (#30) can be set in runinput.yml and are
-   documented (#91, #88)
- * fixed: buffering kwarg was removed from openany() so code is
-   compatible with GromacsWrapper >= 0.8.0 (#107)
- * supported CHARMM and AMBER forcefield (#104)
- * supported wet-octanol solvent boxtype (#98)
- * fixed: using new travis CI settings so CI tests stop failing (#101)
+* renamed package to MDPOW
+* removed all generated docs from package
+* config parser MERGES user runinput.yml with the package defaults
+  (#8)
+* boxtype and minimum distance (#30) can be set in runinput.yml and are
+  documented (#91, #88)
+* fixed: buffering kwarg was removed from openany() so code is
+  compatible with GromacsWrapper >= 0.8.0 (#107)
+* supported CHARMM and AMBER forcefield (#104)
+* supported wet-octanol solvent boxtype (#98)
+* fixed: using new travis CI settings so CI tests stop failing (#101)
+* fixed: GROMACS 2020 fails with "Inconsistency in user input:
+  Could not do a restart with appending because the checkpoint file was not
+  found. Either supply the name of the right checkpoint file or do not use
+  -append": mdpow.run.runMD_or_exit() does not anymore add -append to GROMACS
+  invocation (#128)
 
 
 2017-05-02    0.6.1

mdpow/run.py

@@ -132,7 +132,7 @@ def runMD_or_exit(S, protocol, params, cfg, **kwargs):
             stepout=cfg.getint('mdrun','stepout'),
             nice=cfg.getint('mdrun','nice'),
             nt=cfg.get('mdrun','maxthreads'),
-            cpi=True, append=True)
+            cpi=True)
         simulation_done = mdrun.run_check()
         if not simulation_done:
             # should probably stop

mdpow/tests/testing_resources/states/md_npt/benzene/Equilibrium/water/MD_NPT/local.sh

@@ -16,6 +16,6 @@ PDB=${DEFFNM}.pdb
 
 MDRUN_OPTS=""
 
-mpiexec -n $NCORES mdrun_mpi -nice 19 -v -deffnm ${DEFFNM} -c ${PDB} -cpi -append \
+mpiexec -n $NCORES mdrun_mpi -nice 19 -v -deffnm ${DEFFNM} -c ${PDB} -cpi \
     $MDRUN_OPTS >$OUTPUT 2>&1
 

mdpow/tests/testing_resources/states/md_npt/benzene/Equilibrium/water/MD_relaxed/local.sh

@@ -16,6 +16,6 @@ PDB=${DEFFNM}.pdb
 
 MDRUN_OPTS=""
 
-mpiexec -n $NCORES mdrun_mpi -nice 19 -v -deffnm ${DEFFNM} -c ${PDB} -cpi -append \
+mpiexec -n $NCORES mdrun_mpi -nice 19 -v -deffnm ${DEFFNM} -c ${PDB} -cpi \
     $MDRUN_OPTS >$OUTPUT 2>&1