Hi All,
I've installed fftw-3.3 on my computer when I try to install GROMACS I run
into problems.
A little information:
Here are the values for LDFLAGS and CPPFLAGS
echo $LDFLAGS
-L/home/ramone/mygromacs/lib
The content of this directory is the following:
libfftw3f.a libfftw3f.la* pkgconfig
Problem solved issue with double and single precision versions of gromacs
and fftw.
Ramon
On Tue, Jan 24, 2012 at 2:16 PM, Jose Tusell wrote:
> Hi All,
>
> I've installed fftw-3.3 on my computer when I try to install GROMACS I run
> into problems.
>
> A little inform
I believe ORCA is setup to run with a maximum of 8 processors. Try
running with 8 processors.
The MM part can be run with 1 processor, use -NT 1 as part of your mdrun flags.
Ramon
On Mon, Aug 20, 2012 at 11:38 AM, Jouko Virtanen wrote:
>
> I have been running QM/MM simulations with orca, but w
Source code file: main.c, line: 249
Fatal error:
The 64 subsystems are not compatible
gmxdump gives the same nsteps and init_step. Let me know what you'd need to
file a bug on redmine.
Thanks,
Jose Tusell
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/ma
wrote:
> On 3/09/2011 3:08 PM, Jose Tusell wrote:
>
>> I know this error has been reported before and Mark Abraham suggested to
>> file a bug report on redmine. While starting regular NPT remd on my system
>> I run into the following problem:
>>
>> init_step+n
Hi Mark,
I just posted a bug on redmine for the remd problem that I encountered. I
was as thorough as possible about how to recreate the bug, but if I forgot
some crucial piece of information let me know and I will get it to you as
soon as possible. Thanks for your time.
Jose Tusell
On Sat
ickly converges but after that mdrun run stops with a
segmentation fault. Am I missing something in all of this? Any help
would be greatly appreciated.
Thanks
Jose Tusell
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archi
accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
Why doesn't GROMACS output the energies for certain steps? Step 3 and
steps 5-18 do show any output in the log file. Any ideas why this is
happening?
Thanks,
Jose Tusell
On Mon, Nov 14, 2011 at 7:05
Hi Justin,
Thanks for the input on why this is happening. It sounds a little
suspicious that the energy doesn't change after a few steps of energy
minimization. Do you know of any way that I can find out what is
going on?
Thanks,
Jose Tusell
On Thu, Nov 17, 2011 at 10:58 AM, Jus
I'll try changing the step size first and if that fails I'll try
another algorithm. Thanks for the input.
Jose Tusell
On Thu, Nov 17, 2011 at 11:48 AM, Justin A. Lemkul wrote:
>
>
> Jose Tusell wrote:
>>
>> Hi Justin,
>>
>> Thanks for the input on
m with the protein. However this file is
not created when I run QMMM, I've used the bOpt = true in the mdp
file. Can anyone please offer some help on how to create this LJ
files?
Thanks,
Jose Tusell
On Thu, Nov 17, 2011 at 2:07 PM, swati patel wrote:
> hello,
> I am trying to
file say. Is there !QMMMOpt or only !EnGrad?
> Christoph
>
> On 11/18/2011 06:20 PM, Jose Tusell wrote:
>>
>> Hi Justin,
>>
>> I tried using a larger step size but my system blew up... My guess is
>> that I have a bad starting structure, I'll work on the i
That solved it. In the ORCA manual for version 2.8 it says to use
bOpt = true instead of bOpt = yes. And there is no mention of the mdp
option in the gromacs manual or gromacs online mdp options.
Ramon
On Sun, Nov 20, 2011 at 4:57 PM, Jose Tusell wrote:
> I've tried the bOpt = true.
1 4.7115117 4.2592505 4.6899751
| 53> 1 4.9388400 4.3221569 4.5484522
| 54> 1 5.1027077 4.0887082 4.7342393
| 55> 1 4.9870053 4.3987840 4.6446544
| 56> 1 4.9254298 4.3886098 4.8489299
| 57> 12 5.1316565 4.3423077 5.2266484
| 58> *
| 59> %
t;xQM[i][YY]/0.1,
qm->xQM[i][ZZ]/0.1);
I just don't know where to look for the factor of 10 in the code.
Could anyone point me to this?
Thanks,
Jose Tusell
On Sun, Nov 20, 2011 at 10:00 PM, Justin A. Lemkul wrote:
>
>
> Jose Tusell wrote:
>>
>> When I run gromac
Does anyone know what is going on with the coordinates of the QM
region? Why are they not converted to the correct units? Could
anyone point me to the error?
Thanks
Jose Tusell
On Sun, Nov 20, 2011 at 10:06 PM, Jose Tusell wrote:
> Yes. But where does the code go wrong? I'm rea
subscribe via the World Wide Web, visit
>
> 2. Re: GROMACS/ORCA QMMM (Jose Tusell)
>
> Does anyone know what is going on with the coordinates of the QM
> region? Why are they not converted to the correct units? Could
> anyone point me to the error?
>
> I have not experi
39 NE2 HISH 2 -5.203 -3.793 3.502
ATOM 40 HE2 HISH 2 -5.932 -4.166 4.093
ATOM 41 C HISH 2 -2.329 0.595 1.164
ATOM 42 O HISH 2 -3.089 1.710 1.164
Thanks for any suggestions,
Jose Tusell
--
gmx-users mailing listgmx-users@gromac
Thanks Justin, I used specbond.dat with a 0.15nm searching distance to
create the bond, it seemed to work.
Ramon
On Fri, Jan 22, 2010 at 2:40 PM, Justin A. Lemkul wrote:
>
>
> Jose Tusell wrote:
>
>> Hi,
>>
>> I'm trying to construct diketopiperazine with g
GMX-USERS,
When I try to scale up from 64 processors to 128 processors my simulation
stops running after a few thousand steps. I'm currently using the abe
supercomputer and in the error file I get the following message:
Warning! Rndv Receiver is receiving (3200 < 4800) less than as expected
Any
20 matches
Mail list logo
