Dear Gromacs users,
Can anyone please help me how can I convert a cpt file from a new to an
older Gromacs version?
Thanks
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gle knows them better than I :-)
>
> Mark
>
> On Thu, Jul 4, 2013 at 2:05 PM, Souilem Safa
> wrote:
> > Dear Mark ,
> > Thank you for your quick reply.
> > Could you please provide me a tutorial link example ? I will be grateful.
> > Thank you very much
>
Dear Mark ,
Thank you for your quick reply.
Could you please provide me a tutorial link example ? I will be grateful.
Thank you very much
On 4 July 2013 21:00, Mark Abraham wrote:
> You can't convert a .tpr file's version in either direction. We try to
> make the .tpr format backwards compatibl
Dear Gromacs users,
I tried to do the simulation of a single molecule in cyclohexane, I'm using
gromos 53a6 force field for both molecules.
i did all the minimization steps. After npt, I runned for 25 000 000 steps.
just after around 100 000 steps, the system stops and i got this fatal
error:
Fa
Dear Gromacs users,
I tried to do the simulation of a single molecule in cyclohexane, I'm using
gromos 53a6 force field for both molecules.
i did all the minimization steps. After npt, I runned for 25 000 000 steps.
just after around 100 000 steps, the system stops and i got this fatal
error:
Fa
Dear Justin,
thank you for your reply.
Yes, you are right , I have corrected it already and now it works well.
Cheers,
Safa
On 11 June 2013 09:53, Justin Lemkul wrote:
>
>
> On 6/10/13 8:51 PM, Souilem Safa wrote:
>
>> Dear gromacs users,
>>
>> I'm tryi
Dear gromacs users,
I'm trying to simulate a single molecule in cyclohexane.
I made a box of my molecule using editconf command and next I solvate with
cyclohexane using genbox command :
genbox -cp newbox_DRG.gro -cs chx.gro -p chx_DRG.top -o chx_DRG.gro
I did next a position restraint in the top
;
> On Mon, Jun 10, 2013 at 6:34 AM, Souilem Safa >wrote:
>
> > Dear Gromacs users,
> > I'm still relatively new to molecular modelling.
> > I want to build a OPLSAA toplogy file of my molecule. I have only the pdb
> > file of my molecule.
> > Can any
Dear Gromacs users,
I'm still relatively new to molecular modelling.
I want to build a OPLSAA toplogy file of my molecule. I have only the pdb
file of my molecule.
Can any one help me what detailed steps should I follow to get that topolgy
file.
Many thanks
--
gmx-users mailing listgmx-users@g
Dear Justin,
Thank you very much for your quick response
Cheers,
Safa
On 8 June 2013 12:07, Justin Lemkul wrote:
>
>
> On 6/7/13 11:05 PM, Souilem Safa wrote:
>
>> Dear Gromacs users,
>>
>> I'm aiming to extract a frame file from a reduced trajectory, i did t
Dear Gromacs users,
I'm aiming to extract a frame file from a reduced trajectory, i did the
simulation on gromacs version 4.6.1 and I would like to do my analysis in
gromacs 4.5.6 for availability reasons.
When I entered my command , I got this error :
reading tpx file (md.tpr) version 83 with ve
Dear Justin,
Thank you very much for your quick reply, that is helpful to me
On 4 June 2013 10:05, Justin Lemkul wrote:
>
>
> On 6/3/13 8:54 PM, Souilem Safa wrote:
>
>> Dear Gromacs users,
>> I have simulated my system for two separately 10 ns with continuation
>&g
Dear Gromacs users,
I have simulated my system for two separately 10 ns with continuation
option in order to continue the first 10 ns simulation.
In order to do some analysis , I'm aiming to assemble both trajectory and
tpr files.
I would be very grateful if someone could help me in this issue.
--
Dear gromacs users,
I'm simulating a single molecule in spc water. I'm using a cubic water box
which has 3.4 nm size.
I got the toplogy of my molecule via PRODRG.
After running minimization, NVT , NPT and MD for 10 ns , I checked the
density of water ,it was less than the real value (1000 kg m\S-3\
> --disable-float for double precision and --enable-mpi if you need mpi
>
> remember that fftw and gromacs must have the same precision.
>
> hope this helps you
>
> cheers
>
> Francesco
>
> On Fri, 3 May 2013, at 09:39 AM, Souilem Safa wrote:
> > Dear Gromacs
Dear Gromacs users,
I m aiming to install gromacs 4.5.5 package in in linux Fedora 18. I have
updated the needed compilers and downloaded the fftw-3.3.2.tar.gz and
gromacs4.5.5.tar.gz
I have followed these commands to install:
$ tar -zxvf fftw-3.3.2/
$ cd fftw-3.3.2/
$ ./configure --prefix /home/s
lest action.
>
> Dr. Vitaly Chaban
>
>
>
>
>
>
>
>
> On Thu, May 2, 2013 at 2:40 PM, Souilem Safa
> wrote:
>
> > Dear Gromacs users ,
> > I did the simulation of a single molecule in vacum. I have choosed 10 ns
> > which corresponds to 500 ste
Thank you very much
On 2 May 2013 22:00, Justin Lemkul wrote:
>
>
> On 5/2/13 8:57 AM, Souilem Safa wrote:
>
>> Thank you for your quick answer
>> I have joined here my mdp file and the toplogy one also.
>>
>
> The mailing list does not accept attachment
ation using 2 fs time steps in vacuum. Please provide more
> information about your simulation parameters.
>
> Erik
>
> On 2 May 2013, at 14:40, Souilem Safa wrote:
>
> > Dear Gromacs users ,
> > I did the simulation of a single molecule in vacum. I have choosed
Dear Gromacs users ,
I did the simulation of a single molecule in vacum. I have choosed 10 ns
which corresponds to 500 steps. I was checking the .log file frequently.
I have noticed that the number of steps from 1938900 didn't increases.
When I open a new tab with the top option, I see mdrun s
Dear Gromacs users,
I'm simulating a water-oil interface. From litterature interfacial tension
is determined from pressure tensors as follows:1/2 (Pz - (px+py)/2))*Lz
Where Pz, Px and Py are the pressure tensors in the different axis.
I did a NPT simulation step and I want to check my interfacial
Thank you for your reply :) I will look further
On 25 April 2013 23:18, Justin Lemkul wrote:
>
>
> On 4/25/13 9:10 AM, Souilem Safa wrote:
>
>> Dear Justin,
>> Please I want to ask you for the calculation of interfacial tension from
>> the formula : 1/2 (P
from all the steps and calculate the interfacial
tension which will be only one value? Because it gives different values.
Thank you very much
On 22 April 2013 20:48, Souilem Safa wrote:
> Dear Justin,
> Thank you very much, that is very kind of you :)
>
>
>
> On 22 April 2013 19
Dear Justin,
Thank you very much, that is very kind of you :)
On 22 April 2013 19:42, Justin Lemkul wrote:
>
>
> On 4/21/13 10:37 PM, Souilem Safa wrote:
>
>> Dear Justin,
>>
>> Thanks for your quick reply.
>> I used Gromos 96 force field, I found it well r
2 April 2013 10:37, Justin Lemkul wrote:
>
>
> On 4/21/13 9:30 PM, Souilem Safa wrote:
>
>> Dear Justin,
>> Thank you for your answer, I'm sorry for delay to reply. Actually I'm
>> running a simulation of oil-water interface. I'm using Gromos 53a6 f
el = no; Velocity generation is off
On 19 April 2013 03:28, Justin Lemkul wrote:
>
>
> On 4/18/13 10:51 AM, Souilem Safa wrote:
>
>> Dear Gromacs users,
>> I have runned a semiisotropic NPT simulation for a membrane, I have fixed
>> the pressure i
Dear Gromacs users,
I have runned a semiisotropic NPT simulation for a membrane, I have fixed
the pressure in x and y axis and I varied it only in z axis to keep a
stable interface. But after simulation the obtained interfacial tension is
far bigger than the experimental value. Experimental is 27 m
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