On 10/23/12 12:37 AM, Shima Arasteh wrote:
I have 3 .cpt files in my directory: md.cpt , state.cpt and state_prev.cpt .
What does each one mean?
Use gmxcheck to determine the times present in each.
I guess I need to use the last cpt in my command # mpirun -np 32 mdrun_mpi -s
md.tpr -o
command.
Sincerely,
Shima
From: Erik Marklund
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Sunday, October 21, 2012 10:47 PM
Subject: Re: [gmx-users] Extending simulation
21 okt 2012 kl. 09.22 skrev Shima Arasteh:
Hi again,
>
>I hav
21 okt 2012 kl. 09.22 skrev Shima Arasteh:
> Hi again,
>
> I have done mdrun for 500 steps (10 ns) and got the results. Then I tried
> to extend the simulation for another 500 steps ( I mean the next 10 ns =
> 10 to 20 ns ) using this command:
> # tpbconv -s md.tpr -o md.tpr -extend 10
On 10/21/12 3:22 AM, Shima Arasteh wrote:
Hi again,
I have done mdrun for 500 steps (10 ns) and got the results. Then I tried
to extend the simulation for another 500 steps ( I mean the next 10 ns = 10
to 20 ns ) using this command:
# tpbconv -s md.tpr -o md.tpr -extend 1
# mpiru
Hi again,
I have done mdrun for 500 steps (10 ns) and got the results. Then I tried
to extend the simulation for another 500 steps ( I mean the next 10 ns = 10
to 20 ns ) using this command:
# tpbconv -s md.tpr -o md.tpr -extend 1
# mpirun -np 32 mdrun_mpi -s md.tpr -o md.trr -c md.g
On 29/07/2012 12:26 AM, Bala subramanian wrote:
Friends,
I have a completed simulation for 30ns (done with gro. 4.5.4), Now I
want to extend the simulation for another 30ns. In gromacs page (Ext.
simulations), I found the following procedure to extend the
simulations
tpbconv -s previous.tpr -e
Friends,
I have a completed simulation for 30ns (done with gro. 4.5.4), Now I
want to extend the simulation for another 30ns. In gromacs page (Ext.
simulations), I found the following procedure to extend the
simulations
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr
On 19/03/2012 9:26 PM, priya thiyagarajan wrote:
hello sir,,
initially i did my simulation for 10ns.. after getting result i
analysed it and thought of extending the simulation for another 10ns..
i used following commands..
tpbconv *-s md.tpr -o newmd.tpr -extend 1.00*
*mdrun -s newmd.t
hello sir,,
initially i did my simulation for 10ns.. after getting result i analysed it
and thought of extending the simulation for another 10ns..
i used following commands..
tpbconv *-s md.tpr -o newmd.tpr -extend 1.00*
*mdrun -s newmd.tpr -o md3_2.trr -c md_2.gro -e md_2.edr -g md_2.log -
On 2012-03-02 05:25:01PM +, Steven Neumann wrote:
> Dear Gmx Users,
>
> I run nvt simulation with small timestep with implicit solvent for 500 ps.
> I used particle decomposition for this run (-pd). No I want to extend my
> simulation with different mdp file from the previous nvt using:
>
>
On 21/10/2011 4:51 PM, Chandan Choudhury wrote:
On Fri, Oct 21, 2011 at 10:26 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>> wrote:
On 21/10/2011 3:25 PM, Chandan Choudhury wrote:
Dear gmx users,
A simulation was performed for 50 ns with
; RUN CONTROL
On Fri, Oct 21, 2011 at 10:26 AM, Mark Abraham wrote:
> On 21/10/2011 3:25 PM, Chandan Choudhury wrote:
>
>>
>> Dear gmx users,
>>
>> A simulation was performed for 50 ns with
>>
>> ; RUN CONTROL
>> integrator = md
>> nsteps = 5000
>> dt =
On 21/10/2011 3:25 PM, Chandan Choudhury wrote:
Dear gmx users,
A simulation was performed for 50 ns with
; RUN CONTROL
integrator = md
nsteps = 5000
dt = 0.001
; OUTPUT CONTROL
nstxout = 1000
nstvout =
Dear gmx users,
A simulation was performed for 50 ns with
; RUN CONTROL
integrator = md
nsteps = 5000
dt = 0.001
; OUTPUT CONTROL
nstxout = 1000
nstvout = 1000
nstxtcout= 0
nstlog
Dear Dr.Mark
Thank you very much
you are right
I understood your mean exactly,
On Sun, Apr 10, 2011 at 12:44 PM, Mark Abraham wrote:
> On 10/04/2011 6:04 PM, mohsen ramezanpour wrote:
>
> Dear Dr.Mark
>
> On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham wrote:
>
>> On 10/04/2011 5:40 PM, mohsen ra
On 10/04/2011 6:04 PM, mohsen ramezanpour wrote:
Dear Dr.Mark
On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>> wrote:
On 10/04/2011 5:40 PM, mohsen ramezanpour wrote:
Dear All
I used the following commands accoring to Extending Simulation
Dear Dr.Mark
On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham wrote:
> On 10/04/2011 5:40 PM, mohsen ramezanpour wrote:
>
>> Dear All
>> I used the following commands accoring to Extending Simulation in
>> gromacs/Documentation/how-tos/Extending Simulation
>> to extend my simulation.
>> I entered:
On 10/04/2011 5:40 PM, mohsen ramezanpour wrote:
Dear All
I used the following commands accoring to Extending Simulation in
gromacs/Documentation/how-tos/Extending Simulation
to extend my simulation.
I entered:
tpbconv -s npt-1.tpr-extend 100 -o npt-1-extend.tpr
nohup mpirun -np 4 mdr
Dear All
I used the following commands accoring to Extending Simulation in
gromacs/Documentation/how-tos/Extending Simulation
to extend my simulation.
I entered:
tpbconv -s npt-1.tpr-extend 100 -o npt-1-extend.tpr
nohup mpirun -np 4 mdrun -s npt-1-extend.tpr -cpi npt-1.cpt
Ii run this
- Original Message -
From: Hsin-Lin Chiang
Date: Monday, November 22, 2010 14:51
Subject: Re: [gmx-users] extending simulation without cpt file
To: gmx-users@gromacs.org
> Hi, Mark
>
> So, You mean I can get correct extending simulation without
> using -e ede and -t tr
g simulation?
Hsin-Lin
- Original Message -
From: Yongchul Chung
Date: Thursday, November 4, 2010 10:28
Subject: [gmx-users] extending simulation without cpt file
To: Discussion list for GROMACS users
Hello gmxers,
I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but
erased cpt
ulation?
>
>
>
> Hsin-Lin
>
>
>
> >
>
> >
>
> > - Original Message -
>
> > From: Yongchul Chung
>
> > Date: Thursday, November 4, 2010 10:28
>
> > Subject: [gmx-users] extending simulation without cpt file
>
> > To:
ACS version is 4.0.5.
Am I right to use lines above to do extending simulation?
Hsin-Lin
>
>
> - Original Message -
> From: Yongchul Chung
> Date: Thursday, November 4, 2010 10:28
> Subject: [gmx-users] extending simulation without cpt file
> To: Discussion lis
Thanks Justin! it works now.
Greg
On Wed, Nov 3, 2010 at 7:39 PM, Mark Abraham wrote:
> - Original Message -
> From: Mark Abraham
> Date: Thursday, November 4, 2010 10:38
> Subject: Re: [gmx-users] extending simulation without cpt file
> To: Discussion list fo
- Original Message -
From: Mark Abraham
Date: Thursday, November 4, 2010 10:38
Subject: Re: [gmx-users] extending simulation without cpt file
To: Discussion list for GROMACS users
>
>
> - Original Message -
> From: Yongchul Chung
> Date: Thursday, Novembe
- Original Message -
From: Yongchul Chung
Date: Thursday, November 4, 2010 10:28
Subject: [gmx-users] extending simulation without cpt file
To: Discussion list for GROMACS users
> Hello gmxers,
>
> I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but
>
Yongchul Chung wrote:
Hello gmxers,
I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but
erased cpt file. However, I need to extend the simulation from the end
of the trajectory file. I know this will not be binary identical as
stated here
(http://www.gromacs.org/Docume
Hello gmxers,
I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but
erased cpt file. However, I need to extend the simulation from the end of
the trajectory file. I know this will not be binary identical as stated here
(http://www.gromacs.org/Documentation/How-tos/Extending_Simu
nishap.pa...@utoronto.ca wrote:
Hi,
I am trying to extend my simulation time from 100ns -> 300ns. So I
used the command :
tpbconv -s old.tpr -extend 10 -o new.tpr
but I got this:
Extending remaining runtime of by 20 ps (now 14992 steps)
Writing statusfile with starting step
Hi,
I am trying to extend my simulation time from 100ns -> 300ns. So I
used the command :
tpbconv -s old.tpr -extend 10 -o new.tpr
but I got this:
Extending remaining runtime of by 20 ps (now 14992 steps)
Writing statusfile with starting step 0 and length 14992
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