[gmx-users] RMSD of Different Simulations

[XAvier Periole]

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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