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
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
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
--
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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
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
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
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:
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
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
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
--
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Sorry ...I forget to announce that my potential energy is positive, is it
logical?
From: Zahra M s_zahra_mous...@yahoo.com
To: gmx-users@gromacs.org gmx-users@gromacs.org
Sent: Thursday, December 29, 2011 12:52 PM
Subject: positive potential energy
Hi dear
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 s_zahra_mous...@yahoo.com
*To:* gmx-users@gromacs.org gmx-users@gromacs.org
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 am trying to generate an
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 5:07
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 can be found
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