Martini3 SAXS formfactors

CHANGES/v2.11.md

@@ -6,6 +6,7 @@ This page contains changes that will end up in 2.11
 
   - When using [MOLINFO](MOLINFO.md) with the `WHOLE` flag, PBCs in the following actions will be reconstructed using a minimum spanning tree based on the coordinates stored in the MOLFILE reference pdb.
   - When using the benchmark now it is possible to scale the atom distances in the synthetic atom distribution (the base atomic distance is 1)
+  - [SAXS](SAXS.md) now accepts the `MARTINI_FF` keyword to select the Martini form-factor generation: `MARTINI_FF=2` (default) keeps the existing Martini 2.2 protein and nucleic-acid form factors, while `MARTINI_FF=3` selects Martini 3 protein form factors.
   - Added environment variable `PLUMED_LOG_FILE` to control the log file pathname when runnning with GROMACS (the log file was hardcoded as `PLUMED.OUT`)
 
 ### Changes relevant for developers:

regtest/isdb/rt-saxs-martini3/Makefile

@@ -0,0 +1 @@
+include ../../scripts/test.make

regtest/isdb/rt-saxs-martini3/colvar.reference

@@ -0,0 +1,2 @@
+#! FIELDS time saxs.q-0 saxs.q-1 saxs.q-2 saxs.q-3 saxs.q-4 saxs.q-5 saxs.q-6 saxs.q-7 saxs.q-8 saxs.q-9 saxs.q-10 saxs.q-11 saxs.q-12 saxs.q-13 saxs.q-14 saxs.exp-0 saxs.exp-1 saxs.exp-2 saxs.exp-3 saxs.exp-4 saxs.exp-5 saxs.exp-6 saxs.exp-7 saxs.exp-8 saxs.exp-9 saxs.exp-10 saxs.exp-11 saxs.exp-12 saxs.exp-13 saxs.exp-14
+ 0.000000 0.991783 0.913891 0.770707 0.593473 0.415862 0.264112 0.151598 0.079063 0.038864 0.020385 0.014108 0.013386 0.014365 0.015137 0.014950 0.052725 0.032713 0.012832 0.004555 0.002280 0.001305 0.000722 0.000434 0.000272 0.000257 0.000188 0.000159 0.000081 0.000111 0.000126

regtest/isdb/rt-saxs-martini3/config

@@ -0,0 +1,3 @@
+mpiprocs=4
+type=driver
+arg="--plumed plumed.dat --timestep 0.005 --mf_pdb lyso_cg.pdb"

regtest/isdb/rt-saxs-martini3/plumed.dat

@@ -0,0 +1,30 @@
+# Martini 3 protein SAXS form factors (MARTINI_FF=3) on coarse-grained hen egg-white
+# lysozyme (PDB 4LZT), mapped with martinize2 (martini3001).
+MOLINFO STRUCTURE=lyso_cg.pdb
+
+SAXS ...
+	LABEL=saxs
+	ATOMS=1-304
+	MARTINI
+	MARTINI_FF=3
+
+	QVALUE1=0.0111721000	EXPINT1=0.0527250000
+	QVALUE2=0.0368675000	EXPINT2=0.0327126000
+	QVALUE3=0.0625615000	EXPINT3=0.0128316000
+	QVALUE4=0.0882529000	EXPINT4=0.0045545200
+	QVALUE5=0.1139410000	EXPINT5=0.0022799600
+	QVALUE6=0.1396240000	EXPINT6=0.0013048600
+	QVALUE7=0.1653020000	EXPINT7=0.0007215740
+	QVALUE8=0.1909730000	EXPINT8=0.0004340930
+	QVALUE9=0.2166360000	EXPINT9=0.0002717150
+	QVALUE10=0.2422910000	EXPINT10=0.0002574160
+	QVALUE11=0.2679360000	EXPINT11=0.0001878030
+	QVALUE12=0.2935700000	EXPINT12=0.0001592670
+	QVALUE13=0.3191930000	EXPINT13=0.0000811279
+	QVALUE14=0.3448030000	EXPINT14=0.0001110630
+	QVALUE15=0.3703990000	EXPINT15=0.0001264680
+... SAXS
+
+PRINT ARG=(saxs\.q-.*),(saxs\.exp-.*) FILE=colvar STRIDE=1
+DUMPDERIVATIVES ARG=(saxs\.q-.*) FILE=forces FMT=%.4f
+ENDPLUMED