On 21/07/2012 3:44 PM, radhika jaswal wrote:
When replying to a digest, do change the subject to something useful,
and do not include the entire digest in your email. People have better
things to do than scroll through lots of text to find the relevant part.
Dear Sir,
I am using the ffG43a1
--- On Fri, 20/7/12, gmx-users-requ...@gromacs.org
wrote:
> From: gmx-users-requ...@gromacs.org
> Subject: gmx-users Digest, Vol 99, Issue 79
> To: gmx-users@gromacs.org
> Date: Friday, 20 July, 2012, 7:09 PM
> Send gmx-users mailing list
> submissions to
> gmx-users@gromacs.org
>
> To s
On 7/20/12 11:47 PM, Mark Abraham wrote:
On 20/07/2012 11:32 PM, francesco oteri wrote:
Dear gromacs users (and eventually developers too),
I am trying to debug gromacs and on the gromacs website
http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmer's_Guide#local_index
It is sta
On 19/07/2012 6:24 PM, francesco oteri wrote:
Sorry for the multiple emails but everytime I tried to send the mail I
obtained a message like this:
"The message's content type was not explicitly allowed. Please send
your messages as plain text only. See
http://www.gromacs.org/Support/Mailing_List
On 20/07/2012 4:50 AM, leandro.bor...@usp.br wrote:
Dear users,
I'm currently doing some experiments with the implicit solvation
model running on GPUs with GROMACS.
I can make simple (conventional MD) simulations using the GPUs,
allowing great acceleration by using 1 GPU. However
On 20/07/2012 11:32 PM, francesco oteri wrote:
Dear gromacs users (and eventually developers too),
I am trying to debug gromacs and on the gromacs website
http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmer's_Guide#local_index
It is stated:
"gromacs can be forced to use non assem
Thanks. I hadn't found Table 5.5.
On Jul 20, 2012, at 3:55 PM, Justin Lemkul wrote:
>
>
> On 7/20/12 3:50 PM, Katie Maerzke wrote:
>> Hi all -
>>
>> I am trying to set up a topology file for an ionic liquid force field not
>> included in Gromacs. How do I know which dihedral type correspon
On 7/20/12 3:50 PM, Katie Maerzke wrote:
Hi all -
I am trying to set up a topology file for an ionic liquid force field not
included in Gromacs. How do I know which dihedral type corresponds to which
functional form? For the angular potentials, I assume type 1 is harmonic - is
this corre
Hi all -
I am trying to set up a topology file for an ionic liquid force field not
included in Gromacs. How do I know which dihedral type corresponds to which
functional form? For the angular potentials, I assume type 1 is harmonic - is
this correct?
Thanks
Katie
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gmx-users mailing list
On 7/20/12 2:26 PM, Debashis Sahu wrote:
Dear user,
I have used this RB dihedral for thiourea in
ff-bonded.itp file, which is the error line mentioning below:
dih_THI_H_N_C_S 23.1 -2.1
-21.0 0.0 0.0 0.0
dih_THI_H_N_C
Thanks for you suggestion Peter.
I'll check it out.
Regards,
Shima
- Original Message -
From: Peter C. Lai
To: gmx-users@gromacs.org
Cc:
Sent: Friday, July 20, 2012 9:58 PM
Subject: Re: [gmx-users] Some interactions seem to be assigned multiple times
Did the RTP file include new ato
Dear user,
I have used this RB dihedral for thiourea in
ff-bonded.itp file, which is the error line mentioning below:
dih_THI_H_N_C_S 23.1 -2.1
-21.0 0.0 0.0 0.0
dih_THI_H_N_C_N 20.50160 0.00
On 7/20/12 2:00 PM, Debashis Sahu wrote:
Dear all
I used Gromacs 4.5 for thio-Urea molecule in OPLS-AA force
field, but in grompp step I got an error as follows:
---
Back Off! I just backed up m
Dear all
I used Gromacs 4.5 for thio-Urea molecule in OPLS-AA force
field, but in grompp step I got an error as follows:
---
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
checking input fo
Did you play with DispCorr?
On 2012-07-20 09:46:13AM -0300, Sebastien Cote wrote:
>
> Dear Gromacs users,
>
> My simulations on a POPE membrane using the CHARMM36 parameters are giving
> ''area per lipid'' values well below the experimental value (59.75-60.75
> Angstroms2). Is their someone e
Did the RTP file include new atoms/interactions (angles, dihedrals)? If not
then I don't know. If it did, then you should check to make sure you don't
have the same interactions defined in the .itp files.
On 2012-07-20 09:02:56AM -0700, Shima Arasteh wrote:
>
>
> May this error happen because
May this error happen because of the incorrect value of a new-defined residue
in .rtp file?
Sincerely,
Shima
- Original Message -
From: Peter C. Lai
To: gmx-users@gromacs.org
Cc:
Sent: Wednesday, July 18, 2012 9:00 AM
Subject: Re: [gmx-users] Some interactions seem to be assigne
Dear gromacs users (and eventually developers too),
I am trying to debug gromacs and on the gromacs website
http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmer's_Guide#local_index
It is stated:
"gromacs can be forced to use non assembly routines to do force
calculations (easier to
Dear Gromacs users,
My simulations on a POPE membrane using the CHARMM36 parameters are giving
''area per lipid'' values well below the experimental value (59.75-60.75
Angstroms2). Is their someone else experiencing a similar problem? If yes, how
did you solved it?
I did the following :
I
On 7/20/12 6:46 AM, radhika jaswal wrote:
Dear all,
I did NVT simulations of a number of molecules with double bond. But when i
analysed the results i realised that double bond has been converted to single
bond and sp2 hybridisation has also changed to sp3. I was doing with all bonds
constr
Dear all,
I did NVT simulations of a number of molecules with double bond. But when i
analysed the results i realised that double bond has been converted to single
bond and sp2 hybridisation has also changed to sp3. I was doing with all bonds
constraint option. But when i started with all angle
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