Dear Gromacs users
Hello,
I use gromacs version 4.5.5. I have started with Lysozime in water simulation.
(Justin tutorials)
The md part of simulation was terminated. Now I want to continue the simulation
from the interruption point. Is this command line correct?
mdrun -deffnm md_0_1 -s md
Hi Delara,
To continue a crashed simulation you just need to type in the following
command without deffnm md.
mdrun -s md_0_1.tpr -cpi md_0_1.cpt
You can check the link here:
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
The continuation is down via the .cpt file. the _prev.cpt is
Dear Gromacs users
Hello,
I use gromacs version 4.5.5. I have started with Lysozime in water
simulation. (Justin tutorials)
The md part of simulation was terminated. Now I want to continue the
simulation from the interruption point. Is this command line correct?
mdrun -deffnm md_0_1 -smd_
Yes, I would use the same command to continue the simulation after
stopping with the addition of -cpi
Every time a .cpt is made, the previous one is renamed _prev.cpt so that
you can still get it in case something happened in between the two.
Normally I would use the .cpt but if that doesn't work
mdrun -deffnm md_0_1
If the above crashed, do the following:
mdrun -s md_0_1.tpr -cpi md_0_1.cpt -deffnm md_0_2
This way, pre-crash files are called md_0_1 and post-crash file will be
named md_0_2[.cpt.gro.xtc.trr...]. The simulation will end when it reaches
the number of steps entered in the initi
I found the problem finally. It had to do with the fact that my charge groups
contained atoms in different residue. I just defined one charge group for
every atom, and everything worked.
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Dear All,
I want to do the single point calculations for my systems with gromacs, I
used the method mentioned on the gmx's website.
mdrun -s sp.tpr -rerun configuration.pdb.
However, I have some questions on how to generate the tpr file for single
point calculation. It didn't work if I used a md
Hi users,
I was wondering if there is an easy and quick way to get a frame-wise
binding energy between 2 groups of chains (chain ABC vs DE) in an
existing trajectory. This is not indented to be an actual binding free
energy approach but rather a rough indicator if the binding between two
chai
Hey everyone,
If I ran my simulations with periodic boundary conditions, is there a way
in Gromacs to get a trajectory file tracking the diffusion of the
molecules in the first time frame (i.e. not allow them to exit one side of
the box and reenter the other side)?
If not, can I specify this in t
On 10/30/13 9:31 AM, fantasticqhl wrote:
Dear All,
I want to do the single point calculations for my systems with gromacs, I
used the method mentioned on the gmx's website.
mdrun -s sp.tpr -rerun configuration.pdb.
However, I have some questions on how to generate the tpr file for single
poi
On 10/30/13 11:42 AM, jwill...@andrew.cmu.edu wrote:
Hey everyone,
If I ran my simulations with periodic boundary conditions, is there a way
in Gromacs to get a trajectory file tracking the diffusion of the
molecules in the first time frame (i.e. not allow them to exit one side of
the box and
On 10/30/13 11:26 AM, Knapp Bernhard wrote:
Hi users,
I was wondering if there is an easy and quick way to get a frame-wise binding
energy between 2 groups of chains (chain ABC vs DE) in an existing trajectory.
This is not indented to be an actual binding free energy approach but rather a
roug
Hi,
I was wondering if there is an option or a way to use the algorithm SHAKE
for the water molecules (instead of SETTLE).
Thanks!
Guillaume
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On 10/30/13 12:00 PM, Guillaume Chevrot wrote:
Hi,
I was wondering if there is an option or a way to use the algorithm SHAKE
for the water molecules (instead of SETTLE).
Never tried it, but I would assume
define = -DFLEXIBLE
constraint-algorithm = shake
would do the trick. Of course, tha
Hi,
2013/10/30 Justin Lemkul
>
>
> On 10/30/13 12:00 PM, Guillaume Chevrot wrote:
>
>> Hi,
>>
>> I was wondering if there is an option or a way to use the algorithm SHAKE
>> for the water molecules (instead of SETTLE).
>>
>>
> Never tried it, but I would assume
>
> define = -DFLEXIBLE
> constrai
Dear Gromacs users,
Please somebody help .
editconf computs the incorrect value of "mass of input". I tried to resolve
this problem but failed. Previously I was doing AOt but now I just found that
the molecule OS1 =O2L showing error . Here I posted my A.pdb, RM.rtp
atomtypes.atp. The mass of
Dear Gromacs users,
Please somebody help .
editconf computs the incorrect value of "mass of input". I tried to resolve
this problem but failed. Previously I was doing AOt but now I just found that
the molecule OS1 =O2L showing error . Here I posted my A.pdb, RM.rtp
atomtypes.atp. The mass of
On 10/30/13 2:34 PM, Hari Pandey wrote:
Dear Gromacs users,
Please somebody help .
editconf computs the incorrect value of "mass of input". I tried to resolve
this problem but failed. Previously I was doing AOt but now I just found that the
molecule OS1 =O2L showing error . Here I posted m
On 10/30/13 1:46 PM, Guillaume Chevrot wrote:
Hi,
2013/10/30 Justin Lemkul
On 10/30/13 12:00 PM, Guillaume Chevrot wrote:
Hi,
I was wondering if there is an option or a way to use the algorithm SHAKE
for the water molecules (instead of SETTLE).
Never tried it, but I would assume
de
Michael, thanks for taking the time to comment and have a look.
The real issue I am having is a bit deeper into the topic than that, my last
reply was just an observation on something else. Will summarise what I have
been doing etc.
I have a molecule that are calculating the Gibbs energy of hy
I likely won't have much time to look at it tonight, but you can see
exactly what the option is doing to the topology. run gmxdump on the
tpr. All of the stuff that couple-intramol does is in grompp, so the
results will show up in the detailed listings of the interactions, and
which ones have whi
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