Hi,
In Kalp15_DPPC tutorial, when the InflateGRO methodology is applied to pack the
lipids, I need to follow the iteration while the cutoff value changed to 0.
I' d like to know what settings of EM.mdp file are suggested to get the best
results of doing shrinking steps?
When I set the settings a
Hi,
I edit my topology file for mutating CH --> COH during free energy
calculation.
Since one hydrogen atom attached to carbon disappears, while two O and H
atoms are appearing, I build topology file as follows:
8 opls_169 1TESTO 3 -0.715.9994
opls_1400.1
Dear users,
I make a rectangle bilayer by doubling two equilibrated cubic boxes. But
after minimizing, the system have been crashed. I do not understand why. I
attach the em.mdp below
Thankful for any help !
Thu
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I should add, one is an automated submit system, the others manual quing where you set parmeters (the ones that work), and the system is large around 90 120 90 angstrom box with around 170-180,000 atoms. Still, the que output from the manual submission simply sets -nt 6, and the rest of the input
On 6/15/13 3:56 AM, Shima Arasteh wrote:
Hi,
In Kalp15_DPPC tutorial, when the InflateGRO methodology is applied to pack the
lipids, I need to follow the iteration while the cutoff value changed to 0.
I' d like to know what settings of EM.mdp file are suggested to get the best
results of doi
On 6/15/13 6:21 AM, Kieu Thu Nguyen wrote:
Dear users,
I make a rectangle bilayer by doubling two equilibrated cubic boxes. But
after minimizing, the system have been crashed. I do not understand why. I
attach the em.mdp below
The list does not allow attachments. Either copy and paste or p
Hey :
When increasing the system size like that, make sure that all molecules in
the original box are whole (trjconv -pbc mol). Only then can you, e.g., use
genconf to double the system.
Cheers,
Tsjerk
On Sat, Jun 15, 2013 at 1:49 PM, Justin Lemkul wrote:
>
>
> On 6/15/13 6:21 AM, Kieu Thu N
Hello everybody,
I am trying to simulate a triclinic cristal lattice (4x4x2) with gromacs
(4.5.5) in constant pressure with the Parrinello-Rahman (PR) barostat. the
crystal were previously equilibrated in the NPT ensemble during 1ns at 200K
with berendsen thermostat/barostat
. The crystal initail
Hi gmx users
I really confused that How I determine the distances between center of mass
of a molecules and center of mass of number of other molecules?
Please guide me
thanks a lot
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* Please sear
Is there a way to create a .gro file with the XYZ coordinates of atoms that
are within a specified distance of another atom at each time frame? It
seems that trjconv should be able to do this but I am having a difficult
time figuring it out.
Thank you,
Blake
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View this message in context:
Hi Mark,
I test the simulations again using Berendsen thermostat -- Still, I cannot get
binary identical results.
I do two sets of simulations:
1. Use Gromacs 4.5.2 installed on my personal computer:
Run 2 simulations using the command: mdrun -s md.tpr -deffnm md -nt 1 -cpt 0
-reprod
On Sat, Jun 15, 2013 at 9:00 PM, Cuiying Jian wrote:
>
>
>
>
>
>
>
>
>
> Hi Mark,
>
> I test the simulations again using Berendsen thermostat -- Still, I cannot
> get binary identical results.
> I do two sets of simulations:
> 1. Use Gromacs 4.5.2 installed on my personal computer:
>
4.6.2, I ho
g_select can make such a selection and write it to a group in an index file
that trjconv can then use. But if you want to apply the operation to
multiple frames, then you will need to do some scripting along those lines.
Mark
On Sat, Jun 15, 2013 at 8:05 PM, rankinb wrote:
> Is there a way to
On 6/15/13 1:07 PM, Mahin Saberi wrote:
Hi gmx users
I really confused that How I determine the distances between center of mass
of a molecules and center of mass of number of other molecules?
Use g_dist with suitable index groups.
-Justin
--
Justin
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