Hello everyone,
I am trying to energy minimize a system of 8 polyethylene molecules with 60
units. In literature density of PE is reported 0.9 gr/cm3. Based on this I
need to have each single chain in 3.3 nm^3. If I put this chain in a box of
15*0.5*0.5 =3.75 nm^3 I am close to the density I want.
jojo J wrote:
Hello Justin,
Thanks for your comments and also I really liked your reasoning for
getting no answer from people that are not awake : You are right ;)
Actually, I have no charged particles in my system. All I have is carbon
and hydrogen. I read through the manual meticulou
Hello Justin,
Thanks for your comments and also I really liked your reasoning for getting
no answer from people that are not awake : You are right ;)
Actually, I have no charged particles in my system. All I have is carbon and
hydrogen. I read through the manual meticulously about nonbonded i
I think there have been changes to the way pdb2gmx handles termini, perhaps
related to the impending inclusion of the ffamber ports, but I do not know. I
worked with someone else with this issue, and it was solved by renaming
residues, which seems like a terrible solution. I guess your DNA i
shuai shuai wrote:
Dear all,
thanks for your suggestions. During this NVT simulation, I keep
nanotube rigid. So the temperature should only couple to Nitrogen
instead of the whole system as my original input file. I will try to
couple temperature only to nitrogen to see whether this is the rea
Hi
Thanks, I thought so too.
My command line is: pdb2gmx -f xxx.pdb file The -ter flag is set to default,
i.e. charged termini.
When I use the -ter flag for interactive termini selection and I select NONE
for both N- and C-ter
the message becomes:
Program pdb2gmx, VERSION 4.0.99-dev-2010
Dear all,
thanks for your suggestions. During this NVT simulation, I keep
nanotube rigid. So the temperature should only couple to Nitrogen
instead of the whole system as my original input file. I will try to
couple temperature only to nitrogen to see whether this is the reason.
Many thanks again,
On 2010-07-10 15.56, zhongjin wrote:
Dear users:
I am simulating a CNT in water. In the energy minimization step, I
restrain the CNT by a constant 10e8,because I don't want the CNT to deform.
After minimization,the energy is -44054.835938. Then NVT and NPT
equilibration , at this step,the end C a
Dear users:
I am simulating a CNT in water. In the energy minimization step, I
restrain the CNT by a constant 10e8,because I don't want the CNT to deform.
After minimization,the energy is -44054.835938. Then NVT and NPT equilibration
, at this step,the end C atoms are fixed by a constant 3
On 2010-07-10 12.40, Vitaly Chaban wrote:
Dear Professor van der Spoel:
Don't you have an idea why the average value of pressure appears to be
(always?) slightly larger and (never?) smaller than requested one? I
did not collect the statistics systematically but I often mentioned
this curious fac
Dear Professor van der Spoel:
Don't you have an idea why the average value of pressure appears to be
(always?) slightly larger and (never?) smaller than requested one? I
did not collect the statistics systematically but I often mentioned
this curious fact.
Vitaly
> fluctuations are proportiona
Hi,
if you configure the git version without the "--enable-mpi" flag, it
will turn on threads by default. Depending on the number of processors
you have on your workstation, it will then use these many threads.
You can disable that with
mdrun -nt 1 ...
Carsten
On Jul 10, 2010, at 1:57 AM, Sai
On 2010-07-10 09.47, Vitaly Chaban wrote:
Dear users,
I think the pressure control in gromacs 4.0.7 may have some problems. First ,The
pressure value>fluctuates widely ,even between -7984.377930 and 5920.053711
bar.Second,the average pressure>sometimes is much larger than what I have set,for
Dear Shuai:
Please try to couple temperature for nanotube and nitrogen separately.
BTW, what is your partial charge and how did you construct it?
Good luck!
Dr. Vitaly Chaban
> Recently I met a strong error from gromacs. Therefore I would like to know
> whether you have experienced the same
> Dear users,
> I think the pressure control in gromacs 4.0.7 may have some problems. First
> ,The pressure value >fluctuates widely ,even between -7984.377930 and
> 5920.053711 bar.Second,the average pressure >sometimes is much larger than
> what I have set,for example, I have set ref_p = 1.0
- Original Message -
From: shuai shuai
Date: Saturday, July 10, 2010 2:27
Subject: [gmx-users] Frozen N2 in a very long tube
To: gmx-users@gromacs.org
> Hear all,
>
> Recently I met a strong error from gromacs. Therefore I would
> like to know
> whether you have experienced the same t
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