translation) ?
Thanks,
Shuangxing Dai
On Wed, Jul 28, 2010 at 11:46 AM, Vitaly Chaban wrote:
> Hi Shuangxing,
>
> For my case, I wrote a script just to do +/- LBOX when x>LBOX || x <
> 0. I am not well familiar with polarization algorithm in gromacs but
> it seems not to be a
,
Shuangxing Dai
On Mon, Jul 26, 2010 at 12:26 AM, Vitaly Chaban wrote:
> Hi,
>
> Is there an option in any gromacs utility to apply periodicity to the
> output configuration or trajectory? I want to get all the coordinates
> just within an elementary box, between 0 and LBOX in spite of a
. Does anyone
have idea how to solve this?
Thanks in advance.
Thanks,
Shuangxing Dai
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Thanks for the help.
The error information is: Using Berendsen pressure coupling invalidates the
true ensemble for the thermostat.
Do you have any idea of this information?
Thanks,
Shuangxing Dai
On Jul 12, 2010, at 15:43, "Justin A. Lemkul" wrote:
>
>
> Shuangxing Da
information. When I change and use
Berendson for pressure coupling, there is error information and does not
work.
Anyone have idea about these? Thanks in advance.
Thanks,
Shuangxing Dai
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t/plain; charset=UTF-8; format=flowed
Shuangxing Dai wrote:
> Hi, all,
> I am trying to do anisotropic coupling using Parrinello-Rahman. I
> want to reach the equilibrium state at 1000K, 0.1MPa( 1 bar). However,
> I find that the fluctuation is so large ( p=80.22 bar, T=1007.23 K,
0.01 1.03E+00 2.12E+00 9.95E-03 1.21E-04
100 5.48359 71.5565 91.198 1.25218 300 2.62807 162.926 290.324 3.36594 500
16.6356 1048.76 492.616 5.45231 800 59.3245 594.773 799.314 9.18876 1000
80.2257 626.789 1007.23 11.2159
Thanks in advance,
Shuangxing Dai
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gmx-users mailing listgmx-users
re coupling sensitive
to the initial pressure? I mean if the initial pressure ( in order of GPa),
object pressure is 1 bar ( 1e5 Pa).
*
*
Thanks,
Shuangxing Dai
On Mon, Jun 14, 2010 at 8:50 PM, wrote:
>
>
> Message: 3
> Date: Mon, 14 Jun 2010 19:18:14 -0400
> From: "Justin A.
= 1e-4
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
It seems that the temperature coupling is fast and fluctuation is less that
1%. But the pressure coupling fails. The pressure fluctuates from +1e3 bar
to -1e3 bar. Anyone can help?
Thanks,
Shuangxing
perience in using Parrinello-Rahman? Thanks in advance.
|
|Sure, many people do. What is it that you want to know about it?
|
|-Justin
> Thanks,
> Shuangxing Dai
>
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Departm
advance.
Thanks,
Shuangxing Dai
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BAuthor%5D>
.
The performance there is around 1 ps/day. I do not understand why my
speed is so slow and it seems that Ewald option makes it slow.
Thanks,
Shuangxing Dai
On Thu, Apr 15, 2010 at 10:18 AM, wrote:
> Send gmx-users mailing list submissions to
>gmx-users@gromac
= 1e-4
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
Can anyone help me? Thank you in advance.
Thanks,
Shuangxing Dai
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,
Shuangxing Dai
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need
the breakpoints to be related with the source code so that I can trace
the flow.
Sorry for the last mail that I pressed space accidently...
Thank you in advance.
--
Shuangxing Dai
___
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http
Dear all,
--
Shuangxing Dai
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Dear all,
I was wondering how to debug the executable file mdrun in Xcode. Right now I
can debug it using gdb by following here:
http://oldwiki.gromacs.org/index.php/Programmer's_Guide
But I do not know how to debug it by Xcode. For example, I want to debug this
command:
mdrun -c steep.g96
Hi, all,
I was wondering why I got large pressure after energy minimization. In MD,
the pressure and pressure tensor is defined like ( equation 4.151 in manual):
P=2*(E_kinetic + W)/(3*V), V is volume and W is Virial.
I run a simple system, fcc gold with LJ potential to check
advance.
--
Shuangxing Dai
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Yes, I did one md step and got all non-zero forces.
But for the energy minimization, all the forces are zero, althouth mdrun
command gives non-zero forces.
On Sun, Jun 28, 2009 at 4:23 AM, Florian Dommert <
domm...@icp.uni-stuttgart.de> wrote:
> * Shuangxing Dai [2009-06-27 20:22
atom at
each step? Just like it did to the forces? I use this mdp file and only see
the total energy for each step in the log file.
Thanks again.
On Sat, Jun 27, 2009 at 8:07 PM, Florian Dommert <
domm...@icp.uni-stuttgart.de> wrote:
> * Shuangxing Dai [2009-06-27 18:57:41 -0600]:
The nstfout =1 in mdout.mdp. So this should not be where the problem is.
- Original Message -
From: "Florian Dommert"
To: "Discussion list for GROMACS users"
Sent: Saturday, June 27, 2009 3:20 PM
Subject: Re: [gmx-users] force
___
gmx-use
Hi, all,
I was wondering about the force given by Gromacs. One is in the .trr and
.tpr file. When I read then with gmxdump, they are all zeros:
traj.trr frame 0:
natoms= 24000 step= 0 time=0.000e+00 lambda= 0
box (3x3):
box[0]={ 3.24900e+00, 0.
Hi, all,
I need more digits to input information. But the default format of pdb file
for coordinate is %8.3f. Can I modify the pdbio.c file to achive this goal? Or
is there any other direct ways to input more digits coordinate information in
Gromacs?
Thanks in advance.
Shuangxing Dai_
total
energy to the summation of pair potential since the self energy part is not
easy to decompose.
I will follow your advice. Thanks again.
Shuangxing Dai
- Original Message -
From: "Mark Abraham"
To: "Discussion list for GROMACS users"
Sent: 14 April, 2009 10:21
- Original Message -
From: "Mark Abraham"
To: "Discussion list for GROMACS users"
Sent: 14 April, 2009 8:01 PM
Subject: Re: [gmx-users] Shift Electrostatic Summation
Shuangxing Dai wrote:
Thank you for your help. Yes, when I found the user define part for
elec
force.c since there is no formula for force found. Or I
find the wrong place? And if I want to modify the force formula for Shift,
where is it?
Thank you for your help.
Shuangxing Dai
- Original Message -
From: "Mark Abraham"
To: "Discussion list for GROMACS users"
Hi, all,
I was wondering to modify Shift electrostatic summation to a new one. The
origin Shift form in Gromacs is like 1/r-1/Rc (Rc is cut-off), I need to modify
to erfc(alpha*r)/r-erfc(alpha*Rc)/Rc, and the original long-range correction of
Shift in code shift_util.c is q^2/(2*Rc) ( someth
is
the problem.
Shuangxing Dai
- Original Message -
From: "David van der Spoel"
To: "Discussion list for GROMACS users"
Sent: 13 April, 2009 11:15 AM
Subject: Re: [gmx-users] shell molecular dynamics
Shuangxing Dai wrote:
Hi, all,
I am doing shell molecular
Hi, all,
I am doing shell molecular dynamics and I have read the sw.itp. Now my
question is:
1. For the shell "atom", what element should be used in .pdb file, since the
77-78th digits of pdb file is element symbol ?
2. What does the 1 in [ polarization ] part mean in sw.itp?
3. Is it reasonab
- Original Message -
From: "Mark Abraham"
To: "Discussion list for GROMACS users"
Sent: 27 March, 2009 5:01 PM
Subject: Re: [gmx-users] How to add another electrostatic summation
methodinGromacs
Shuangxing Dai wrote:
Yes, but I still cannot write out the
for your kindly help.
Shuangxing Dai
- Original Message -
From: "Mark Abraham"
To: "Discussion list for GROMACS users"
Sent: 26 March, 2009 4:56 PM
Subject: Re: [gmx-users] How to add another electrostatic summation methodin
Gromacs
Shuangxing Dai wrote:
Thank
this
Wolf method can, so I cannot simply use Gromacs to do my simulation. The
question is which files needed to be modified if I want to add a new one? Is
there any direct way? Or I should read all the whole code?
Thank you very much.
Shuangxing Dai
On Mon, Mar 23, 2009 at 11:55 PM, Mark Abraham
Hi, all,
I was wondering how to add another electrostatic summation method--Wolf
summation into Gromacs. Wolf summation is a treatment for summation of
Coulombic energy. Since the formula of total potential energy for each ion is
known, how to add this into Gromacs? According to Chapter 7, I
> > Subject: Re: [gmx-users] combination rules -- the part
> aboutthecombinationrules
> >
> > Shuangxing Dai wrote:
> > > Yes, "add parameters for crystalline zinc oxide, which require
> > > Buckingham nonbonded interactions", that is what I am doing. I think
very much.
2009/2/22 Mark Abraham
> Shuangxing Dai wrote:
>
>> No. I only changed 3 lines in ffgmxnb.itp. But there are hundreds of lines
>> of error informaion like this:
>> ERROR 77 [file ffgmxnb.itp, line 144]:
>> Trying to add LJ (SR) while the default nonbond type
ge -
> From: "Mark Abraham"
> To: "Discussion list for GROMACS users"
> Sent: Friday, February 20, 2009 6:02 PM
> Subject: Re: [gmx-users] combination rules -- the part aboutthe
> combinationrules
>
>
> > Shuangxing Dai wrote:
>
ary 20, 2009 6:02 PM
Subject: Re: [gmx-users] combination rules -- the part aboutthe
combinationrules
Shuangxing Dai wrote:
Thanks for your answer. I changed the non-bond parameters in ffgmxnb.itp.
like
; ij func abc6
Zn O2 ... . But error occur
Thanks for your answer. I changed the non-bond parameters in ffgmxnb.itp. like
; ij func abc6
Zn O2 ... .
But error occured..
ERROR 1 [file ffgmxnb.itp, line 270]:
Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
ER
Hello,
I was wondering how to set up parameters for interactions between two
different atoms A and B. Since for Gromacs parameters are defined to each kind
of atom, I cannot specify parameters between A and B. For Buckingham potential,
the rule was:
A_ij=(A_ii * A_jj)^(1/2)
So anyone know
Hi, all gmx users:
I am doing a simulation with NaCl (and ZnO, GaN). I start with the .pdb
file. But the Gromacs cannot recognize my new atom, such as Na, Cl. How to add
new atoms to Gromacs?
I am going to use periodical boundary conditions and LJ potential, shell
model , apply loading
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