Den 2020-03-15 kl. 20:53, skrev Afsane Farhadi:
hi all I generated a box 4×4×4 (nm) with 100 molecules methyldiethanolamine by
insert-molecules , forcefield is opls . after energy minimization the potential
energy decreased but had a positive value . is my simulation wrong ? help me
please
S
hi all I generated a box 4×4×4 (nm) with 100 molecules methyldiethanolamine by
insert-molecules , forcefield is opls . after energy minimization the potential
energy decreased but had a positive value . is my simulation wrong ? help me
please
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Hi,
Thanks for your help, Justin!
Regards,
Mahsa
On Sun, Feb 25, 2018 at 5:53 PM, Justin Lemkul wrote:
>
>
> On 2/25/18 10:15 AM, Mahsa wrote:
>
>> Dear Justin,
>>
>> Thank you for your reply!
>>
>> In general, is it a good approach to first use steep algorithm for EM and
>> then to further mi
On 2/25/18 10:15 AM, Mahsa wrote:
Dear Justin,
Thank you for your reply!
In general, is it a good approach to first use steep algorithm for EM and
then to further minimize do EM with cg algorithm, on the output structure?
I usually don't find multiple steps of EM needed in most cases, but
Dear Justin,
Thank you for your reply!
In general, is it a good approach to first use steep algorithm for EM and
then to further minimize do EM with cg algorithm, on the output structure?
Could you please comment on my question about the mdp files and pbc as
well? Actually, you mentioned here:
On 2/25/18 9:26 AM, Mahsa wrote:
Dear Mark,
Thank you for your reply. However, this is not clear for me yet since I
read this in the tutorial from Justin:
"There are two very important factors to evaluate and determine if EM was
successful. The first is the potential energy (printed at the en
Dear Mark,
Thank you for your reply. However, this is not clear for me yet since I
read this in the tutorial from Justin:
"There are two very important factors to evaluate and determine if EM was
successful. The first is the potential energy (printed at the end of the EM
process, even without -v)
Hi,
Even if there are minima on the surface that have negative energy (which
will depend how the model was developed, which you should look into)
there's no reason to expect an arbitrary starting configuration will find
one after a steepest descent search. A tangled pile of strings will stay
tangl
Hello,
I want to simulate a box of polymer (32 chains) with salt. I started with
one chain of the polymer in the box. However, after the energy
minimisation, the energy is still positive. I found the discussion in the
link below very similar to the problem I have:
https://mailman-1.sys.kth.se/pip
Hi,
On Thu, Jun 22, 2017 at 11:30 AM Emran Heshmati wrote:
> Hi all
> I run two simulations on a 16 aa peptide under the same conditions
> (forcefield, simulation duration, ...) except the solvent in one of
> the simulations was TFE instead of water. The potential energy in the TFE
> containing
Hi all
I run two simulations on a 16 aa peptide under the same conditions
(forcefield, simulation duration, ...) except the solvent in one of
the simulations was TFE instead of water. The potential energy in the TFE
containing system was positive (about 14 Kj/mol), while in water
containing sys
Hi allI run two simulations on a 16 aa peptide under the same conditions
(forcefield, simulation duration, ...) except the solvent in one of the
simulations was TFE instead of water. The potential energy in the TFE
containing system was positive (about 14 Kj/mol), while in water containing
Hi allI run two simulations on a 16 aa peptide under the same conditions
(forcefield, simulation duration, ...) except the solvent in one of the
simulations was TFE instead of water. The potential energy in the TFE
containing system was positive (about 14 Kj/mol), while in water containing
Hi allI run two simulations on a 16 aa peptide under the same conditions
(forcefield, simulation duration, ...) except the solvent in one of the
simulations was TFE instead of water. The potential energy in the TFE
containing system was positive (about 14 Kj/mol), while in water containing
Hey Daniel :)
This doesn’t make sense as the molecule should fly apart with always
> positive PE.
>
>
You need a force to make things fly apart, but the force has little to do
with the absolute PE. It's the gradients that do it. And as Justin points
out, your system can choose between positive PE
On 8/28/14, 2:04 PM, Dan Sponseller wrote:
Hello everyone.
I am still fairly new to gromcs but I have researched this well.
I am getting a positive potential energy (my bond energy is always positive) no
matter how long I run my simulation. I also get this when doing minimizations.
Even jus
Hello everyone.
I am still fairly new to gromcs but I have researched this well.
I am getting a positive potential energy (my bond energy is always positive) no
matter how long I run my simulation. I also get this when doing minimizations.
Even just one molecule set at know minimum conformation
On 8/8/14, 7:25 AM, neha bharti wrote:
I am trying to perform MD for protein ligand protein complex in popc lipid
with charmm36 force field and also follow Justin A. Lemkul tutorial.
After Adding Ion
genion -s ions.tpr -o pro_POPC_sol_ions.gro -p topol.top -pname NA -np 1
-nname CL
I preform
I am trying to perform MD for protein ligand protein complex in popc lipid
with charmm36 force field and also follow Justin A. Lemkul tutorial.
After Adding Ion
genion -s ions.tpr -o pro_POPC_sol_ions.gro -p topol.top -pname NA -np 1
-nname CL
I preform energy minimization step. In energy minimi
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