Re: [gmx-users] creating index for first hydration layer water molecules

On 6/10/15 2:20 AM, Sahithya S Iyer wrote: Thanks for the reply Justin. I have tried the following: g_select -f prodrun.xtc -s prodrun.tpr -n index.ndx -os size.xvg - oc cfrac.xvg -oi index.dat -select '"Nearby water" resname SOL and within 0.35 of group Protein' Note that with trajectories

Re: [gmx-users] creating index for first hydration layer water molecules

Thanks for the reply Justin. I have tried the following: g_select -f prodrun.xtc -s prodrun.tpr -n index.ndx -os size.xvg - oc cfrac.xvg -oi index.dat -select '"Nearby water" resname SOL and within 0.35 of group Protein' But there is a syntax error. Could you please tell me where i could be going

Re: [gmx-users] creating index for first hydration layer water molecules

On 6/9/15 5:11 AM, Sahithya S Iyer wrote: Dear Users, The first hydration layer, to the best of my understanding, is the first minimum in the protein (backbone)-water radial distribution function. How do I create an index for the water molecules in the first hydration layer? The hydration l

[gmx-users] creating index for first hydration layer water molecules

Dear Users, The first hydration layer, to the best of my understanding, is the first minimum in the protein (backbone)-water radial distribution function. How do I create an index for the water molecules in the first hydration layer? Cheers -- Gromacs Users mailing list * Please search the arch