Dear Justin
2014-02-25 19:07 GMT+01:00 Justin Lemkul :
>
>
> On 2/25/14, 12:56 PM, Francesca Vitalini wrote:
>
>> Dear Justin,
>>
>> Thanks for your answer.
>> However I noticed that I had made a mistake and there is no definition of
>> NAC in GROMOS53a6, it was the .rtp file of OPLS-AA I was lo
>> I have looked up "tabulated potential" in the manual and also the suggested
>> document, neither of them actually helps the situation.
Why do they not?
Dr. Vitaly V. Chaban
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Dear Gromacs users,
we want to simulateHSA protein using8 processors. Usually with our available
system 10ns simulation on 8 processors lasts 2-3 days.
This time we submitted 10 ns simulation, after almost 6 days it has finished
but when we look at md.log file, only 179411 steps has been complete
On 2/26/14, 4:08 AM, Francesca Vitalini wrote:
Dear Justin
2014-02-25 19:07 GMT+01:00 Justin Lemkul :
On 2/25/14, 12:56 PM, Francesca Vitalini wrote:
Dear Justin,
Thanks for your answer.
However I noticed that I had made a mistake and there is no definition of
NAC in GROMOS53a6, it was
On 2/26/14, 12:51 AM, gupta.rakesh082 wrote:
Dear allI performed MD simulation of lipid bilayer on my desktop it is giving
correct results and negative potential energy (~ -10^5) but when I ran the
same simulation on a server using multi thread (-nt 8), It is giving
positive potential energy (~
On 2/26/14, 4:31 AM, delara aghaie wrote:
Dear Gromacs users,
we want to simulateHSA protein using8 processors. Usually with our available
system 10ns simulation on 8 processors lasts 2-3 days.
This time we submitted 10 ns simulation, after almost 6 days it has finished
but when we look at md
if the system sends a termination request to MDRUN, it stops the main
cycle and writes down the summary of the run.
Dr. Vitaly V. Chaban
On Wed, Feb 26, 2014 at 10:31 AM, delara aghaie wrote:
> Dear Gromacs users,
> we want to simulateHSA protein using8 processors. Usually with our available
Dear Dr. Justin,
Thank you for pointing out the details of error. I have missed out the
version of GROMACS I have been using and so I would like to let you know
that my version is 4.5.7. In this version ffnonbonded.itp file of the
gromos53a6.ff forcefield doesnt have pairtypes fr LJ-14 interaction
On 2/26/14, 7:05 AM, lalithkumar wrote:
Dear Dr. Justin,
Thank you for pointing out the details of error. I have missed out the
version of GROMACS I have been using and so I would like to let you know
that my version is 4.5.7. In this version ffnonbonded.itp file of the
gromos53a6.ff forcefiel
I am using gromacs 4.6.5. Surprisingly system is stable at such high
potential energy. I created bilayer system using packmol then solvated it
with water using genbox.
I did energy minimization using following command
grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tpr
mdrun -c -v -deffnm min
On 2/26/14, 10:50 AM, gupta.rakesh082 wrote:
I am using gromacs 4.6.5. Surprisingly system is stable at such high
potential energy. I created bilayer system using packmol then solvated it
with water using genbox.
I did energy minimization using following command
grompp -f em.mdp -c cerblayer.
Dear All,
I ran a NVT simulation with a layer of oil+vaccuum.
Because of periodic boundary condition, there are some molecules on the top
of vaccuum layer.
Now I want to increase the vaccum thickness so that I can add some water in
it.
Is there a simple way to do that?
The molecules on the top of
editconf -box X Y Z
Dr. Vitaly V. Chaban
On Wed, Feb 26, 2014 at 7:58 PM, decaiyu wrote:
> Dear All,
>
> I ran a NVT simulation with a layer of oil+vaccuum.
> Because of periodic boundary condition, there are some molecules on the top
> of vaccuum layer.
> Now I want to increase the vaccum thi
Hello Everyone,
I have been using the Martini CG forcefield to simulate phase separation in
a bilayer containing DPPC/DUPC/Chol at a ratio of 1:1:.5. Though this does
phase separate at 295 K, when I use mdp files based on
http://md.chem.rug.nl/cgmartini/images/parameters/exampleMDP/martini_v2.x_ex
Hello Everyone,
I have been using the Martini CG forcefield to simulate phase separation in
a bilayer containing DPPC/DUPC/Chol at a ratio of 1:1:.5. Though this does
phase separate at 295 K, when I use mdp files based on
http://md.chem.rug.nl/cgmartini/images/parameters/exampleMDP/martini_v2.x_ex
Residue 2 is just alanine,the most standard amino acid ever.
Any help?
Francesca.
Il 26/feb/2014 11:58 "Justin Lemkul" ha scritto:
>
>
> On 2/26/14, 4:08 AM, Francesca Vitalini wrote:
>
>> Dear Justin
>>
>>
>> 2014-02-25 19:07 GMT+01:00 Justin Lemkul :
>>
>>
>>>
>>> On 2/25/14, 12:56 PM, Franc
EM RUNSteepest Descents converged to machine precision in 2820 steps,but did
not reach the requested Fmax < 10.Potential Energy = -2.9268122e+05Maximum
force = 1.9479546e+02 on atom 123Norm of force =
6.3931437e+00grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tprmdrun -c
-v -deffnm
EM RUN
Steepest Descents converged to machine precision in 2820 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -2.9268122e+05
Maximum force = 1.9479546e+02 on atom 123
Norm of force = 6.3931437e+00
grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tpr
mdrun -c -
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