From 63bce38bbdb3356035b48a215cb0cb5d8c17f44d Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Mon, 24 Oct 2016 21:02:11 +0200
Subject: [PATCH] MultiRMSD: some more doc and removed NOPBC keyword
---
src/colvar/MultiRMSD.cpp | 33 ++++++++++++++++++++++++++++++++-
1 file changed, 32 insertions(+), 1 deletion(-)
diff --git a/src/colvar/MultiRMSD.cpp b/src/colvar/MultiRMSD.cpp
index 5a157fbe6..72e62b945 100644
--- a/src/colvar/MultiRMSD.cpp
+++ b/src/colvar/MultiRMSD.cpp
@@ -111,7 +111,37 @@ positions. Here distances are calculated using the \ref DRMSD measure.
MULTI-RMSD REFERENCE=file.pdb TYPE=MULTI-DRMSD
\endverbatim
-...
+in this case it is possible to use the following DRMSD options in the pdb file using the REMARK syntax:
+\verbatim
+NOPBC to calculate distances without PBC
+LOWER_CUTOFF=# only pairs of atoms further than LOWER_CUTOFF are considered in the calculation
+UPPER_CUTOFF=# only pairs of atoms further than UPPER_CUTOFF are considered in the calculation
+\endverbatim
+as shown in the following example
+
+\verbatim
+REMARK NOPBC
+REMARK LOWER_CUTOFF=0.1
+REMARK UPPER_CUTOFF=0.8
+ATOM 2 O ALA 2 -0.926 -2.447 -0.497 1.00 1.00 DIA O
+ATOM 4 HNT ALA 2 0.533 -0.396 1.184 1.00 1.00 DIA H
+ATOM 6 HT1 ALA 2 -0.216 -2.590 1.371 1.00 1.00 DIA H
+ATOM 7 HT2 ALA 2 -0.309 -1.255 2.315 1.00 1.00 DIA H
+ATOM 8 HT3 ALA 2 -1.480 -1.560 1.212 1.00 1.00 DIA H
+ATOM 9 CAY ALA 2 -0.096 2.144 -0.669 1.00 1.00 DIA C
+ATOM 10 HY1 ALA 2 0.871 2.385 -0.588 1.00 1.00 DIA H
+TER
+ATOM 12 HY3 ALA 2 -0.520 2.679 -1.400 1.00 1.00 DIA H
+ATOM 14 OY ALA 2 -1.139 0.931 -0.973 1.00 1.00 DIA O
+ATOM 16 HN ALA 2 1.713 1.021 -0.873 1.00 1.00 DIA H
+ATOM 18 HA ALA 2 0.099 -0.774 -2.218 1.00 1.00 DIA H
+ATOM 19 CB ALA 2 2.063 -1.223 -1.276 1.00 1.00 DIA C
+ATOM 20 HB1 ALA 2 2.670 -0.716 -2.057 1.00 1.00 DIA H
+ATOM 21 HB2 ALA 2 2.556 -1.051 -0.295 1.00 1.00 DIA H
+ATOM 22 HB3 ALA 2 2.070 -2.314 -1.490 1.00 1.00 DIA H
+END
+\endverbatim
+
*/
//+ENDPLUMEDOC
@@ -123,6 +153,7 @@ void MultiRMSD::registerKeywords(Keywords& keys){
keys.add("compulsory","REFERENCE","a file in pdb format containing the reference structure and the atoms involved in the CV.");
keys.add("compulsory","TYPE","MULTI-SIMPLE","the manner in which RMSD alignment is performed. Should be MULTI-OPTIMAL, MULTI-OPTIMAL-FAST, MULTI-SIMPLE or MULTI-DRMSD.");
keys.addFlag("SQUARED",false," This should be setted if you want MSD instead of RMSD ");
+ keys.remove("NOPBC");
}
MultiRMSD::MultiRMSD(const ActionOptions&ao):
--
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