Re: [gmx-users] Normal Mode Analysis with Gromacs 4.6

[mcfc1301]

Hello Everyone， 

I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot but
find little useful. 
My Gromacs was installed in a Linux cluster. 

Follows is my steps to do normal mode analysis: 

• pdb2gmx -ignh -ff  forcefield  -f protein.pdb -o mut.gro -p topol.top 
• editconf -f mut.gro -o box.gro -d 1.5 
• grompp -f em.mdp -c box.gro -p topol.top -o em.tpr 
• mdrun -s em.tpr -deffnm em -c em.g96 -v 
• grompp -f nm.mdp -c em.g96 -o nm.tpr 
  ---WARNING 1 [file nm.mdp]: 
The switching range for PME-Switch should be 5% or
less, energy 
conservation will be good anyhow, since ewald_rtol =
1e-05

I have taken advises from the forum that I should not genbox and should use
cg instead steep for em in order to do Normal Mode Analysis, but now I am
facing problem of PME-Switch. 

Does anyone have any experience on this? 
  
Thanks in advance. 

Kevin 


==Attached is em.mdp and nm.mdp= 
em.mdp 

define  =  -DFLEXIBLE 
constraints =  none 
integrator  =  cg 
dt  =  0.002; ps ! 
nsteps  =  400 
nstlist =  10 
ns_type =  grid 
rlist   =  1.0 
coulombtype =  PME 
rcoulomb=  1.0 
vdwtype =  cut-off 
rvdw=  1.4 
optimize_fft=  yes 
emtol   =  1000 
emstep  =  0.01 

--- 
nm.mdp
constraints =  none 
integrator  =  nm 
dt  =  0.002; ps ! 
nsteps  =  400 
nstlist =  10 
ns_type =  grid 
rlist   =  1.2 
coulombtype =  PME-Switch 
rcoulomb=  1.0 
vdwtype =  Cut-off 
rvdw=  1.4

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Re: [gmx-users] Compiling GROMACS with fftw3

[mcfc1301]

I am currently dealing with a new problem. That is I could not specify the
path to install the gromacs.
As I am not on the sudoer list, I must specify a home directory.
According to the installation guide, 

cmake .. -DGMX_INSTALL_PREFIX=/path/to/install 

should work, but it does not.

Hope anyone has experience on this minor problems.

Thanks!

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