g_confrms -f1 conf1.gro -f2 conf2.gro -n1 ind1.ndx -n2 ind2,ndx should
do the trick.
On Feb 9, 2010, at 1:27 AM, Mark Abraham wrote:
On 09/02/10 10:20, V Hariharan wrote:
Hello All,
I've taken the average peptide structure from two different MD
simulations using g_rmsf. Is there a method for calculating the RMSD
between those two structures? The only difference between the two
peptides is a single residue mutation. Thanks.
You may need to use trjconv to strip both down to a common matching
set of (say) CA atoms. Then g_rms -s A.gro -f B.gro.
Mark
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