[gmx-users] How to calculate enthalpy

Hi I want calculate the enthalpy of water molecule corresponding to protein folded and unfolded state. How much a single water molecule (enthalpy and free energy) contribute in folding ? Can we calculate enthapy from g_energy? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gro

Re: [gmx-users] How to calculate enthalpy

Thanks Vitaly but how?? let's say the difference between unfolded to folded protein is 100 water molecules. What is the correct procedure to calculate (theoretically) the entrapy correspond to single water molecule for stabilizing/destabilizing the protein. help me > Sure, you can. > > > > Dr.

[gmx-users] entropy calculation

Hi gmx users I took a natural protein fold and unfolded with simulated annealing molecular dynamics (SAMD). Now I have folded and unfolded structure. I want to calculate statistically entropy difference of the two system. Can we do with gromacs??? what is the correct protocol ?? best pooja --

Re: [gmx-users] entropy calculation

Thanks Justin > > > On 7/16/13 4:30 AM, pooja_gu...@nccs.res.in wrote: >> Hi gmx users >> >> I took a natural protein fold and unfolded with simulated annealing >> molecular dynamics (SAMD). Now I have folded and unfolded structure. I >> want to calculate statistically entropy difference of the two

Re: [gmx-users] entropy calculation

Hi Justin When i used g_anaeig option for the calulation, i choose system as an option i got an error "Segmentation fault (core dumped)" > > > On 7/16/13 4:30 AM, pooja_gu...@nccs.res.in wrote: >> Hi gmx users >> >> I took a natural protein fold and unfolded with simulated annealing >> molecular d

Re: [gmx-users] entropy calculation

thanks for reply i am using Gromacs 4.5.5 version command g_anaeig -v *.trr -entropy -s *.tpr -extr -f *.pdb -rmsf -3d -comp -Pooja > > > On 7/17/13 7:28 AM, pooja_gu...@nccs.res.in wrote: >> Hi Justin >> >> When i used g_anaeig option for the calulation, i choose system as an >> option i got an

Re: [gmx-users] entropy calculation

I used system (0) for g-covar. Pooja > > > On 7/17/13 7:42 AM, pooja_gu...@nccs.res.in wrote: >> thanks for reply >> >> i am using Gromacs 4.5.5 version >> command >> g_anaeig -v *.trr -entropy -s *.tpr -extr -f *.pdb -rmsf -3d -comp >> > > What was the g_covar command used to generate the eigenv

Re: [gmx-users] extraction of PDB from clusters.pdb

try trjconv to extract the structures pooja > You can do it by using simple shell scripting > On Jul 17, 2013 12:58 AM, "Shine A" wrote: > >> Sir, >> >> Using g_cluster I clustered snapshots in md trajectory using the >> command as follows >> >> g_cluster -s sd_7.tpr -f traj7.trr -dist r

Re: [gmx-users] entropy calculation

okk This may be very basic question. I took a natural pdb and unfold with SAMD. I ran simulation for 10ns. I picked up one unfolded structure from the trj and solvated with water. I ran em for full system. now i am calculating the entropy. I afraid if i missed something. I am doing this first tim

Re: [gmx-users] entropy calculation

i took only single structure > > > On 7/17/13 8:09 AM, pooja_gu...@nccs.res.in wrote: >> okk >> >> This may be very basic question. >> I took a natural pdb and unfold with SAMD. I ran simulation for 10ns. I >> picked up one unfolded structure from the trj and solvated with water. I >> ran em for fu

Re: [gmx-users] entropy calculation

thank justin > > > On 7/17/13 8:19 AM, pooja_gu...@nccs.res.in wrote: >> i took only single structure >>> > > You can't calculate entropy from a single structure. Please investigate > the > literature. > > -Justin > >>> >>> On 7/17/13 8:09 AM, pooja_gu...@nccs.res.in wrote: okk This

[gmx-users] script to add water in protein

Hi I want to add water molecule in my structure. Do anyone have idea how to add water molecules in protein structure. I little aware of python. How the gromacs spc216 add the water molecule. Can i get the code for the same? pooja -- gmx-users mailing listgmx-users@gromacs.org http://lists.g

Re: [gmx-users] script to add water in protein

Thanks I am looking for code (python, C++), not gromacs command line. pooja > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html > > > On Mon, Aug 12, 2013 at 4:09 PM, wrote: > >> Hi >> >> I want to add water molecule in my structure. Do anyone have