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

Re: [gmx-users] entropy calculation

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 may be very basic question. I took a natural p

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

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 full system. now i am calculating the entropy. I a

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

On 7/17/13 7:56 AM, pooja_gu...@nccs.res.in wrote: I used system (0) for g-covar. Most likely, g_anaeig is running out of memory. Try using some subset of the system, like the protein only or its backbone. -Justin On 7/17/13 7:42 AM, pooja_gu...@nccs.res.in wrote: thanks for reply i

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] entropy calculation

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 eigenvector .trr file? What group did you choose for analysis

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

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 error "Segmentation fault (core dumped)" Please provide the exact sequence of commands you used, copied and pasted from your terminal. Please a

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 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

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 system. Can we do with groma

[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 --