On 4/2/16 11:36 PM, Brett wrote:
Dear All,
Before when I got a MD crashed, I do the following to continue it,
"gmx tpbconv -s md_0_1.tpr -extend 0 -o md_0_1extending0ps.tpr
gmx mdrun -deffnm md_0_1extending0ps -cpi md_0_1_prev.cpt -reprod -v &"
Recently I have a crashed MD, and when I do "g
Dear All,
Before when I got a MD crashed, I do the following to continue it,
"gmx tpbconv -s md_0_1.tpr -extend 0 -o md_0_1extending0ps.tpr
gmx mdrun -deffnm md_0_1extending0ps -cpi md_0_1_prev.cpt -reprod -v &"
Recently I have a crashed MD, and when I do "gmx tpbconv -s md_0_1.tpr -extend
0
Hi,
On Thu, 31 Mar 2016 19:00 Michael Shirts wrote:
> > One more question: why does the free energy code have to use its own
> kernel?
There are some aspects that are only used in (some kinds of) free-energy
calculations e.g. soft-core options. So maybe coulomb-only transitions have
an optimiz
thanks so much. I modified the nvt.mdp file as follow:
tc-grps= SOL; two coupling groups - more accurate
tau_t= 0.1; time constant, in ps
ref_t= 298.15 ; reference temperature, one
for each group, in K
--
Gromacs
On 4/1/16 10:51 PM, Brett wrote:
Thanks Justin.
Based on your answer, here I would like to ask,
Suppose there is a PDB for a protein-ligand, and it is already known ligand
would lead extremely significant conformation change of that specific
protein. Based on the protein-ligand PDB, I would l
On 4/2/16 2:11 AM, sun wrote:
Hello Gromacs Users I have already posted this query but in the absence of
any suggestion, I am posting it again. I hope someone will help me. I am
going to do protein-peptide MD using Justin's protein-ligand tutorial (ff
gromos43A1, GROMACS version 5.0). My ligand
On 4/2/16 12:58 PM, Saeed Nasiri wrote:
Dear users
I used the "define= -DFLEXIBL" option and the problem within the energy
minimization step has been solved. However, there is another problem in the
nvt equilibration step. please help me with this problem!
Thanks in advanced.
* ~/Desktop
Dear users
I used the "define= -DFLEXIBL" option and the problem within the energy
> minimization step has been solved. However, there is another problem in the
> nvt equilibration step. please help me with this problem!
>
Thanks in advanced.
* ~/Desktop/water_box $ gmx_mpi grompp -f nvt.mdp -c
Dear Nicolas and Mark:
Indeed, I have spent the last 2 days testing the plumed Hrex code for gromacs
5.1.2. This is likely the way that I will go. I was looking for an alternate
route because I am cautious of bugs and I thought that if I could do it easily
in tested gromacs + a bit of code that
Dear Irem,
You may want to run the trajectory through trjconv and translate it, or use
e.g. -pbc whole, so that the protein is intact at frame 1. Then you can run
trjconv -pbc nojump on the resulting trajectory. This usually requires a bit of
trial and error.
Kind regards,
Erik
> On 31 Mar 20
Dear Vitaly,
Isn’t this a case of a tumbling ice cube
(https://en.wikipedia.org/wiki/Flying_ice_cube)? The solution is usually to
change the comm-removal to include angular motions.
Kind regards,
Erik
On 31 Mar 2016, at 22:22, VITALY V. CHABAN
mailto:vvcha...@gmail.com>> wrote:
I simulate a
See: https://groups.google.com/forum/#!topic/plumed-users/eJ0xpnHPb_s and
https://github.com/GiovanniBussi/plumed2/tree/v2.2-hrex
Nicolas
2016-04-02 12:09 GMT+02:00 Mark Abraham :
> Hi,
>
> On Fri, Apr 1, 2016 at 11:39 PM Christopher Neale <
> chris.ne...@alum.utoronto.ca> wrote:
>
> > Dear deve
Hi,
On Fri, Apr 1, 2016 at 11:39 PM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> Dear developers:
>
> Is it possible with only a small amount of work to modify calc_delta() in
> src/programs/mdrun/repl_ex.cpp to add another case to re->type such that
> the program sends the coordina
thanks again.
I did the recommended option in the grompp command , but there a problem
with minimization step. the error is
"Water molecule starting at atom x can not be settled".
I checked the previous emails and I did a few things but I can't solve it.
In the previous emails, it was recommended
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