On 6/15/12 4:08 AM, Satish Kamath wrote:
Dear Users,
I've managed to obtain a well equilibrated box of 2,3 dihydroxynaphthalene
at 450K (melting point=437K) and 1 bar pressure. I've calculated hydrogen
bond distance using g_hbond and it comes to 0.267 nm. I've also calculated
the density and i
Dear Users,
I've managed to obtain a well equilibrated box of 2,3 dihydroxynaphthalene
at 450K (melting point=437K) and 1 bar pressure. I've calculated hydrogen
bond distance using g_hbond and it comes to 0.267 nm. I've also calculated
the density and it comes to 1229 kg/m3 (solid density = 1120 k
On 6/13/12 4:29 AM, Satish Kamath wrote:
Dear Sir,
I removed the H-H 1-4 interaction from pairs and this seems to have lowered
the potential a lot to 10^2 from 9000 but is still positive. But is it a
valid thing to do?
Haphazardly deleting energetic terms to produce a more desirable energy
Dear Sir,
I removed the H-H 1-4 interaction from pairs and this seems to have lowered
the potential a lot to 10^2 from 9000 but is still positive. But is it a
valid thing to do?
Satish Kamath
IISc Bangalore
India
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Positive-Poten
Dear Sir,
Thank you once again for your reply. I ran the simulation longer. The
potential energy has stabilized to around 9000 and does not show a
decreasing trend. Also the max hydrogen bond distance is around 0.3 nm. The
density of the solid is 1120 kg/m3, couldn't get the density data after its
On 6/12/12 8:26 AM, Satish Kamath wrote:
Dear Sir,
Thank you for your reply. I just ran NPT and the potential stabilizes at
around +9000. The charge distribution change has reduced a lot of potential
but it is still positive. My NPT ran for 1ns.
Then either the topology is still not suitabl
Dear Sir,
Thank you for your reply. I just ran NPT and the potential stabilizes at
around +9000. The charge distribution change has reduced a lot of potential
but it is still positive. My NPT ran for 1ns.
Satish Kamath
IISc Bangalore
--
View this message in context:
http://gromacs.5086.n6.nabb
On 6/12/12 4:13 AM, Satish Kamath wrote:
I've refined the charge distribution.
nr type resnr resid atom cgnr charge- prodrg (NEW) mass
1OA 1 F09 OAD 1 -0.117 (-0.596)15.9994
2 H 1 F09 HAD 10.027 (+0.469
I've refined the charge distribution.
nr type resnr resid atom cgnr charge- prodrg (NEW)mass
1OA 1 F09 OAD 1 -0.117 (-0.596) 15.9994
2 H 1 F09 HAD 10.027 (+0.469) 1.0080
3 C
Dear Sir,
Thank you for your response. I've read the paper and will look into the
charge distribution.
Thank you once again.
Satish Kamath
IISc Bangalore
India
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Positive-Potential-Energy-after-equilibration-tp4998327p4998337.html
On 29/12/2011 8:24 PM, Zahra M wrote:
Sorry ...I forget to announce that my potential energy is positive, is
it logical?
No.
*From:* Zahra M
*To:* "gmx-users@gromacs.org"
*Sent:* Thursday, December 29, 2011 12:52 PM
*
Sorry ...I forget to announce that my potential energy is positive, is it
logical?
From: Zahra M
To: "gmx-users@gromacs.org"
Sent: Thursday, December 29, 2011 12:52 PM
Subject: positive potential energy
Hi dear all
I'm simulating a system containing CNT,
On 16/11/2011 1:18 AM, Harpreet Basra wrote:
Hi Mark,
Thanks for the quick reply. But i have already done what u suggested.
On 15/11/2011 6:06 PM, Harpreet Basra wrote:
> Hi
> I am still stuck with same problem of obtaining positive potential
> energy.
> >>On 11/11/2011 5:
Hi Mark,
Thanks for the quick reply. But i have already done what u suggested.
>
> On 15/11/2011 6:06 PM, Harpreet Basra wrote:
> > Hi
> > I am still stuck with same problem of obtaining positive potential
> > energy.
> > >>On 11/11/2011 5:07 PM, Harpreet Basra wrote:
> > >> Hi
> > >>
> > >> I a
hi,
I am still stuck with same problem of obtaining positive potential energy.
>>On 11/11/2011 5:07 PM, Harpreet Basra wrote:
>> Hi
>>
>> I am trying to generate an equilibrated box of 216 TFE molecules.To
>> generate the 216 TFE molecule box i performed following steps:
>
>A suggested workflow c
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