Thanks a lot!
*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*
On Thu, Feb 23, 2017 at 9:10 PM, Justin Lemkul wrote:
>
>
> On 2/23/17 9:07 AM, Anurag Dobhal wrote:
>
>> Dear Justin,
>>
>> I would like to know wea
On 2/23/17 9:07 AM, Anurag Dobhal wrote:
Dear Justin,
I would like to know weather the parameters below are correct for NVT
equilibiration whicle doig a simulation in vaccum ?
define = -DPOSRES ; position restrain the protein
If you don't have solvent, there's no reason to restrain anything
Dear Justin,
I would like to know weather the parameters below are correct for NVT
equilibiration whicle doig a simulation in vaccum ?
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 5 ; 2 * 5 = 100 ps
dt = 0.002 ; 2 fs
;
Thank you !
*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*
On Thu, Feb 23, 2017 at 7:09 PM, Justin Lemkul wrote:
>
>
> On 2/23/17 8:29 AM, Anurag Dobhal wrote:
>
>> Thank you. Should I not use PME and PBC while
On 2/23/17 8:29 AM, Anurag Dobhal wrote:
Thank you. Should I not use PME and PBC while performing simulations in
Vaccum ?
No, you should not. Use no PBC and infinite cutoffs (all cutoffs set to zero)
to mimic vacuum conditions. Otherwise you're simulating some type of diffusely
occupied
Thank you. Should I not use PME and PBC while performing simulations in
Vaccum ?
--
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On 2/23/17 8:23 AM, Anurag Dobhal wrote:
Dear gromacs users,
I am Simulating a polymer chain having 20 monomer units. I am doing the
simulation in the vaccum (I am not solvating the system). The total charge
in my polymer chain is +9 and I am not nutrealizing the system as I was
suggested earl
Dear gromacs users,
I am Simulating a polymer chain having 20 monomer units. I am doing the
simulation in the vaccum (I am not solvating the system). The total charge
in my polymer chain is +9 and I am not nutrealizing the system as I was
suggested earlier that if we are simulating a system in a
Dear gromacs users,
I am Simulating a polymer chain having 20 monomer units. I am doing the
simulation in the vaccum (I am not solvating the system). The total charge
in my polymer chain is +9 and I am not nutrealizing the system as I was
suggested earlier that if we are simulating a system in a
