Shuangxing Dai wrote:
Thank you for your help. I checked all the force field, all of them are
with default non-bond params in LJ. So I still need to try new solution.
I add my non bond parameters in the .top file generated. Force field
files were not changed. Then I use grompp, the error was:
f you need other atoms as well, you will need to find
> a consistent force field, probably or completely LJ
> or completely Buckingham.
>
> Berk
>
> > Date: Thu, 26 Feb 2009 09:22:26 +1100
> > From: mark.abra...@anu.edu.au
> > To: gmx-users@gromacs.org
100
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] combination rules -- the part
> aboutthecombinationrules
>
> Shuangxing Dai wrote:
> > Yes, "add parameters for crystalline zinc oxide, which require
> > Buckingham nonb
Shuangxing Dai wrote:
Yes, "add parameters for crystalline zinc oxide, which require
Buckingham nonbonded interactions", that is what I am doing. I think I
have changed all the necessary parts for the Buckingham potential. Is
there any direct way to accomplish my goal?
No, because it's not a
Yes, "add parameters for crystalline zinc oxide, which require Buckingham
nonbonded interactions", that is what I am doing. I think I have changed
all the necessary parts for the Buckingham potential. Is there any direct
way to accomplish my goal?
Since in ffgmxnb.itp, all the nonbond_params are L
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 is Buck.ham (SR)
Sure, this is predictable. This force field's files com
for GROMACS users
Sent: Sunday, February 22, 2009 3:03 PM
Subject: RE: [gmx-users] combination rules -- the part
aboutthecombinationrules
Hi,
Is line 68 one of the lines you have added, or another one?
Berk
> From: shuangxing...@gmail.com
> To: gmx-users@gromacs.org
>
Hi,
Is line 68 one of the lines you have added, or another one?
Berk
> From: shuangxing...@gmail.com
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] combination rules -- the partaboutthe
> combinationrules
> Date: Sun, 22 Feb 2009 14:55:21 -0700
>
&g
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
Shuangxing Dai wrote:
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 non
, February 18, 2009 11:39 AM
Subject: RE: [gmx-users] combination rules -- the part about the
combinationrules
Hi,
No pairtypes are for bonded pair interactions,
not for combinations of non-bonded interactions.
The manual tells you how to do this:
[ nonbond_params ]
A_ii A_jj 2 a b
> Subject: [gmx-users] combination rules -- the part about the combination
> rules
>
> For LJ interactions, use [ pairtypes ]. For Coulombics there is
> unfortunately no analogous solution. I am not clear about exactly what
> you want to do. What "parameters"
For LJ interactions, use [ pairtypes ]. For Coulombics there is
unfortunately no analogous solution. I am not clear about exactly what
you want to do. What "parameters" are you interested in, or by this do
you just mean LJ and Q?
Chris.
-- original message --
Hello,
I was wondering ho
Shuangxing Dai wrote:
I also have problem in installing xmgr. I use MacOSX 10.5.5. I type
./configure and got this error messege:
ecme222-96-dhcp:xmgr-4.1.2 ssx$ ./configure
creating cache ./config.cache
checking host system type... configure: error: can not guess host type;
you must speci
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
priyanka srivastava wrote:
Dear Mark,
Thanx for your reply.
Chapter 5 describes it, but I guess that is described
in a more general way! GORMOS87 uses a different kind
of scaling which is not mentioned in chapter 5 and
hence I am just curious to know whether GROMOS96 also
uses same scaling sc
Dear Mark,
Thanx for your reply.
Chapter 5 describes it, but I guess that is described
in a more general way! GORMOS87 uses a different kind
of scaling which is not mentioned in chapter 5 and
hence I am just curious to know whether GROMOS96 also
uses same scaling scheme as is used for GROMOS87 o
priyanka srivastava wrote:
Dear All,
I would be really thankful if somebody could tell me
the combination rules used for creating the
[pairtypes] in lipid.itp (i.e. the 1,4 interactions)
in GROMOS96. Is it the same as is used in GROMOS87?
Does the chapter five of GROMACS manual not describe th
Dear All,
I would be really thankful if somebody could tell me
the combination rules used for creating the
[pairtypes] in lipid.itp (i.e. the 1,4 interactions)
in GROMOS96. Is it the same as is used in GROMOS87?
eagerly waiting for the reply,
regards,
Pri...
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