Yes that is fine. I don't want to go later than 5 though.
Jason
On 28-Sep-06, at 3:02 PM, [EMAIL PROTECTED] wrote:
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Today's Topics:
1. energy minimization end too early! (zzhwise1)
2. QMMM interface ([EMAIL PROTECTED])
3. Re: energy minimization end too early! (Tsjerk Wassenaar)
4. Re: Re: water molecules in vacuum simulation (David Mobley)
5. Job Vacancy -MolNaC University of Salerno (andrea correa)
6. cardiolipin / Cytochrome C (Viswanadham Sridhara)
7. defining new residues? ([EMAIL PROTECTED])
8. Re: defining new residues? (Dongsheng Zhang)
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Message: 1
Date: Thu, 28 Sep 2006 20:38:56 +0800 (CST)
From: zzhwise1 [EMAIL PROTECTED]
Subject: [gmx-users] energy minimization end too early!
To: gmx-users gmx-users@gromacs.org
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=gb2312
hi everyone
today ,I do minimization with my system,my system with two face
to face monolayers composed of ch3(ch2)13cooh,
when i set the molecular as CHO group,it pass smoothly,because i
want to pull the upper layer ,so i set the upper layer group DHO
that has the same parameters with CHO itp , but the mdrun only
reached 22th step and finished normally,which is too few to 5000
steps!
i want why !
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Message: 2
Date: Thu, 28 Sep 2006 14:01:31 +0100
From: [EMAIL PROTECTED]
Subject: [gmx-users] QMMM interface
To: gmx-users@gromacs.org
Message-ID: [EMAIL PROTECTED]
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Dear Gromacs users,
I have been using Pcgamess for QM calculations, which is a very fast
(and free) program, and has some QMMM capabilities(but a size limit of
about 1000 atoms ). I just found out that Gromacs now has QMMM
capabilities with CPMD, Gaussian and Gamess(UK). Does any one know
whether a Gromacs-PcGamess QMMM interface is planned? It would be
great
for those of us with small research budgets, and who cannot afford the
comercial QM codes.
Pedro
Enviado por https://webmail.ufp.pt
--
Message: 3
Date: Thu, 28 Sep 2006 15:08:47 +0200
From: Tsjerk Wassenaar [EMAIL PROTECTED]
Subject: Re: [gmx-users] energy minimization end too early!
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
[EMAIL PROTECTED]
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Hi Zzhwise1,
Energy minimization does not need to run all steps. You define a
maximum number, but maybe the minimum is already reached before that.
On the other hand, the energy may have gone to infinity, which usually
puts an end to minimization. Check the energies you get during/after
minimization. Check for overlaps, bad starting structures, bad box,
etc.
Tsjerk
On 9/28/06, zzhwise1 [EMAIL PROTECTED] wrote:
hi everyone
today ,I do minimization with my system,my system with two
face to face
monolayers composed of ch3(ch2)13cooh,
when i set the molecular as CHO group,it pass smoothly,because i
want to
pull the upper layer ,so i set the upper layer group DHO that has
the same
parameters with CHO itp , but the mdrun only reached 22th step and
finished
normally,which is too few to 5000 steps!
i want why !
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½á »é Éú Óý ³± ½Ó õà ÖÁ¡¡Ð¡ Ìì ¶ì Ë® ħ ·½ ϲ Ó »Æ ½ð ÖÜ
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Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
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Message: 4
Date: Thu, 28 Sep 2006 08:42:46 -0700
From: David Mobley [EMAIL PROTECTED]
Subject: Re: [gmx-users] Re: water molecules in vacuum simulation
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
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This may be naive, but have you defined
