No, GROMACS is reporting that the conditions that produced the supplied
checkpoint are different from those of the current mdrun. This is not a
problem - you could have done the equivalent of first run with the
conditions of the second, after all - but GROMACS noting the event is
perhaps useful whe
On Sat, Dec 14, 2013 at 10:52 AM, Keerthana S.P Periasamy <
keerthanas...@yahoo.com> wrote:
>
>
>
>
>
> On Saturday, December 14, 2013 10:51 AM, Keerthana S.P Periasamy <
> keerthanas...@yahoo.com> wrote:
>
> Hai
>
> initially I used 4processors for mdrun and due to some power
> fluctuat
On Saturday, December 14, 2013 10:51 AM, Keerthana S.P Periasamy
wrote:
Hai
initially I used 4processors for mdrun and due to some power
fluctuations i have restatrted my file using 8 processors. I am getting the
message as follows. I want to know whether I am correct?
#nod
On Fri, Dec 13, 2013 at 2:01 PM, Jones de Andrade wrote:
> Hi all.
>
> We are having some problem running g_tcaf here. It keeps yielding
> "segmentation faults".
>
> We first thought it was because of the single-precision calculations
> of the first run, or the exceedingly large trajectory file. B
On Fri, Dec 13, 2013 at 3:38 PM, chem grad wrote:
> Actually... yes, I may have spoken too soon... I can see Gromacs on my
> machine, but I am still struggling to get it to run properly.
>
> I cannot convince cygwin to source the gromacs files properly (well, at
> least I think that's the problem
On 13.12.2013 21:38, chem grad wrote:
I cannot convince cygwin to source the gromacs files properly (well, at least I think that's the
problem). When I enter "luck" into the command line it returns the "luck: command
not found" error message.
Also, both commands I have entered (pdb2gmx and mdru
Actually... yes, I may have spoken too soon... I can see Gromacs on my machine,
but I am still struggling to get it to run properly.
I cannot convince cygwin to source the gromacs files properly (well, at least I
think that's the problem). When I enter "luck" into the command line it returns
th
On 13.12.2013 18:01, chem grad wrote:
Thank you so much!
Gromacs seems to be installed properly now.
but mdrun doesn't work, right?
M.
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Hi all.
We are having some problem running g_tcaf here. It keeps yielding
"segmentation faults".
We first thought it was because of the single-precision calculations
of the first run, or the exceedingly large trajectory file. Both were
changed for a second trial, which still yielded the same erro
Many thanks Justin.
Ehsan
- Original Message -
From: "Justin Lemkul"
To: "Discussion list for GROMACS users"
Sent: Friday, December 13, 2013 10:21:59 AM
Subject: Re: [gmx-users] OPLS force field parameters
On Fri, Dec 13, 2013 at 1:16 PM, Ehsan Sadeghi wrote:
> Thanks Justin.
>
> I a
On Fri, Dec 13, 2013 at 1:16 PM, Ehsan Sadeghi wrote:
> Thanks Justin.
>
> I already added the description in the ffbonded.itp, but nothing is shown
> in the topol file. I am not sure to put atom names (e.g. C9 C10) or atom
> type (C C)? However, I tried both and non of them worked. I don't kn
Thanks Justin.
I already added the description in the ffbonded.itp, but nothing is shown in
the topol file. I am not sure to put atom names (e.g. C9 C10) or atom type (C
C)? However, I tried both and non of them worked. I don't know what I am doing
wrong and I appreciate if you could help me
Thank you so much!
Gromacs seems to be installed properly now.
From: Mirco Wahab [via GROMACS] [ml-node+s5086n5013279...@n6.nabble.com]
Sent: Thursday, December 12, 2013 3:25 AM
To: Summers, Kelly
Subject: Re: Installing Gromacs 4.6.3 using Cygwin
On 11.12.2013 1
Hi,
Here you go!
http://pubs.acs.org/doi/abs/10.1021/jp003919d
On Fri, Dec 13, 2013 at 8:42 PM, pp0ta187 wrote:
> Thank you Justin for a quick response.
>
> Although, I can not find the spoken reference in the manual, could you
> please point in which version is it?
>
>
>
> --
> View this mess
Thank you Justin for a quick response.
Although, I can not find the spoken reference in the manual, could you
please point in which version is it?
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Calculating-atom-charges-for-ester-tp5013305p5013310.html
Sent from the GROMACS
got you. Thanks again!
Santo
-
K. P. Santo
Post doctoral fellow
Department of Chemistry
University of North Carolina at Chapel Hill
Chapel Hill, NC, USA
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292p5013308.html
Sent from the GROMAC
On Fri, Dec 13, 2013 at 6:38 AM, pp0ta187 wrote:
> Dear forum users,
>
> I am new to MD and looking for help and a little tutorial how to create a
> .gro/.pdb file and calculate atom charges for a molecule I can not find
> online. I have assembled the molecule's .itp file and I seek help how to
>
Dear list subscribers,
I am very happy to announce that also next year, the traditional
Molecular Modelling Workshop in Erlangen (formerly known as "Darmstadt
workshop") takes place on March, Monday 17th to Wednesday 19th, 2014.
Starting on Monday after lunch should allow to avoid travelling on
Dear forum users,
I am new to MD and looking for help and a little tutorial how to create a
.gro/.pdb file and calculate atom charges for a molecule I can not find
online. I have assembled the molecule's .itp file and I seek help how to
calculate charges with OPLS.
molecule: 4-Methoxyphenyl dichl
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