Re: [gmx-users] Re: SMD - reproducibility

[André Farias de Moura]

there should be an extra option in your mdrun command line if
reproducibility is an issue:

-[no]reprod  bool   no  Try to avoid optimizations that affect binary
reproducibility

the value of -reprod is set to no by default, turn on that option and
trajectories should be the same.

best

Andre

On Fri, Apr 26, 2013 at 9:25 AM, Steven Neumann wrote:

> Thanks anyway. I will try tu pull it 20-40 times to tell something.
>
> Steven
>
> On Fri, Apr 26, 2013 at 1:23 PM, Thomas Schlesier  >wrote:
>
> > Don't know. One idea i have: Take a flexible and a relative rigid system
> > and perform simulations with the same starting conditions (-> using -t
> > *.cpt). I would imagine that for the flexible system the trajectories
> start
> > earlier to deviate, since more stuff could happen (system is more
> flexible
> > -> greater configurational space). For the rigid system the
> configurational
> > space is smaller, so the probability is higher to always follow the same
> > trajectory if one starts with a predefinded velocity and direction.
> > But don't know if this is true, but it's the first thing which comes to
> my
> > mind.
> >
> >
> > Am 26.04.2013 14:01, schrieb gmx-users-requ...@gromacs.org:
> >
> > Thanks for this. I think option 2 is more reasonable. However, still do
> not
> >> know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD
> >> simulations...
> >>
> >> On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesier **
> >> >wrote:
> >>
> >> >Think i now understand your question. Forget what i wrote before.
> >>> >I could imagine the the 'grompp -t npt.cpt' part is a problem.
> >>> >If the simulations would be numerical reproducible, one should get the
> >>> >same results. As they are not, the results will differ somewhat (would
> >>> >think the more, the longer you simulate). But two different
> simulations
> >>> >would be more equal to each other, than two simulations which start
> with
> >>> >different velocity distributions for the particles.
> >>> >
> >>> >
> >>> >If you're interested in an stochastic analysis of your system (meaning
> >>> >simulations which are not equal - performing many pulling experiments
> in
> >>> >reality, one would also have many different starting points) you could
> >>> do
> >>> >two things:
> >>> >1) Run a look npt simulation, and use different frames to start the
> SMD
> >>> >simulations. From each frame the particles should have a different
> >>> velocity
> >>> >distribution and the results of the SMD simulations should also
> differ.
> >>> >(Depending on how many SMD simulations you want to perform, this might
> >>> get
> >>> >expensive, since the starting frame for SMD should be separated by
> more
> >>> >then a few ps.)
> >>> >2) Dump the 'npt.cpt' file and randomly determine new velocities for
> >>> each
> >>> >particle at the start of each SMD simulation. Since each simulation
> has
> >>> a
> >>> >different velocity distribution, the SMD simulation wont be the same.
> >>> This
> >>> >approach has only one weak point. Due to assigning new random
> velocities
> >>> >you destroy the thermal equilibrium of the system. But if the system
> was
> >>> >well equilibrated before, this distrubance should only be small and
> >>> after
> >>> >the first 100-200 ps of the SMD simulaton the system is in thermal
> >>> >equilibrium. If the complete SMD simulation is much longer (couple of
> >>> ns),
> >>> >the interesting stuff would happen longer after the inital simulation
> >>> time
> >>> >with the destroyed equilibrium.
> >>> >
> >>> >Hope this helps
> >>> >Thomas
> >>> >
> >>> >
> >>> >
> >>> >Am 26.04.2013 12:00, schriebgmx-users-request@**gromacs.org<
> schriebgmx-users-requ...@gromacs.org>
> >>> :
> >>> >
> >>> >Dear Users,
> >>>
>  >>
>  >>I am running my puling simulations of ligand with constant velocity.
>  First
>  >>I minimize and equilibrate my system:
>  >>
>  >>grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
>  >>mdrun -s em.tpr -deffnm em
>  >>grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o
>  nvt298.tpr
>  >>mdrun -s nvt298.tpr -deffnm nvt298
>  >>grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
>  >>topol.top -o npt298.tpr
>  >>mdrun -s npt298.tpr -deffnm npt298
>  >>
>  >>Then I run 10 pulling simulations with the same mdp file:
>  >>
>  >>grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t
>  npt298.cpt
>  >>-o
>  >>pull_1.tpr
>  >>mpiexec mdrun -s pull_1.tpr -deffnm pull_1
>  >>
>  >>...
>  >>
>  >>grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t
>  npt298.cpt
>  >>-o
>  >>pull_10.tpr
>  >>mpiexec mdrun -s pull_10.tpr -deffnm pull_10
>  >>
>  >>
>  >>I get 3 different (but similar) profiles (Force vs time) with 10
>  >>simulations as some of them produce exactly the same results... In
>  another
>  >>system with the same methodology I get 10 si

Re: [gmx-users] Re: SMD - reproducibility

[rajendra kumar]

I am not sure but different force profiles may be due to the
non-equilibrium relaxation problem. The path on the energy landscape during
the non-equilibrium simulations depends on the pulling rate and/or
relaxation of any unknown coordinates correlated with pulling coordinates.
If during pulling, correlated coordinates will not be able to relax
completely, high energy path is more likely on the energy landscape. Effect
of relaxations can be tested by performing simulations at several reduced
pulling rate. Also, there are several literature available on the effect of
pulling rate during simulations.

With best regards,
Rajendra

On Fri, Apr 26, 2013 at 5:31 PM, Steven Neumann wrote:

> Thanks for this. I think option 2 is more reasonable. However, still do not
> know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD
> simulations...
>
> On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesier  >wrote:
>
> > Think i now understand your question. Forget what i wrote before.
> > I could imagine the the 'grompp -t npt.cpt' part is a problem.
> > If the simulations would be numerical reproducible, one should get the
> > same results. As they are not, the results will differ somewhat (would
> > think the more, the longer you simulate). But two different simulations
> > would be more equal to each other, than two simulations which start with
> > different velocity distributions for the particles.
> >
> >
> > If you're interested in an stochastic analysis of your system (meaning
> > simulations which are not equal - performing many pulling experiments in
> > reality, one would also have many different starting points) you could do
> > two things:
> > 1) Run a look npt simulation, and use different frames to start the SMD
> > simulations. From each frame the particles should have a different
> velocity
> > distribution and the results of the SMD simulations should also differ.
> > (Depending on how many SMD simulations you want to perform, this might
> get
> > expensive, since the starting frame for SMD should be separated by more
> > then a few ps.)
> > 2) Dump the 'npt.cpt' file and randomly determine new velocities for each
> > particle at the start of each SMD simulation. Since each simulation has a
> > different velocity distribution, the SMD simulation wont be the same.
> This
> > approach has only one weak point. Due to assigning new random velocities
> > you destroy the thermal equilibrium of the system. But if the system was
> > well equilibrated before, this distrubance should only be small and after
> > the first 100-200 ps of the SMD simulaton the system is in thermal
> > equilibrium. If the complete SMD simulation is much longer (couple of
> ns),
> > the interesting stuff would happen longer after the inital simulation
> time
> > with the destroyed equilibrium.
> >
> > Hope this helps
> > Thomas
> >
> >
> >
> > Am 26.04.2013 12:00, schrieb gmx-users-requ...@gromacs.org:
> >
> > Dear Users,
> >>
> >> I am running my puling simulations of ligand with constant velocity.
> First
> >> I minimize and equilibrate my system:
> >>
> >> grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
> >> mdrun -s em.tpr -deffnm em
> >> grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr
> >> mdrun -s nvt298.tpr -deffnm nvt298
> >> grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
> >> topol.top -o npt298.tpr
> >> mdrun -s npt298.tpr -deffnm npt298
> >>
> >> Then I run 10 pulling simulations with the same mdp file:
> >>
> >> grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt
> >> -o
> >> pull_1.tpr
> >> mpiexec mdrun -s pull_1.tpr -deffnm pull_1
> >>
> >> ...
> >>
> >> grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt
> >> -o
> >> pull_10.tpr
> >> mpiexec mdrun -s pull_10.tpr -deffnm pull_10
> >>
> >>
> >> I get 3 different (but similar) profiles (Force vs time) with 10
> >> simulations as some of them produce exactly the same results... In
> another
> >> system with the same methodology I get 10 similar but different
> profiles.
> >> I
> >> am wondering why in this case only 3 types are possible... Shall I try
> >> grompp without -t npt.cpt ?
> >>
> >> Steven
> >>
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
> > Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > * Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> http://www.gromacs.org/Support/Mailing_Lists>
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mail

Re: [gmx-users] Re: SMD - reproducibility

[Steven Neumann]

Thanks anyway. I will try tu pull it 20-40 times to tell something.

Steven

On Fri, Apr 26, 2013 at 1:23 PM, Thomas Schlesier wrote:

> Don't know. One idea i have: Take a flexible and a relative rigid system
> and perform simulations with the same starting conditions (-> using -t
> *.cpt). I would imagine that for the flexible system the trajectories start
> earlier to deviate, since more stuff could happen (system is more flexible
> -> greater configurational space). For the rigid system the configurational
> space is smaller, so the probability is higher to always follow the same
> trajectory if one starts with a predefinded velocity and direction.
> But don't know if this is true, but it's the first thing which comes to my
> mind.
>
>
> Am 26.04.2013 14:01, schrieb gmx-users-requ...@gromacs.org:
>
> Thanks for this. I think option 2 is more reasonable. However, still do not
>> know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD
>> simulations...
>>
>> On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesier> >wrote:
>>
>> >Think i now understand your question. Forget what i wrote before.
>>> >I could imagine the the 'grompp -t npt.cpt' part is a problem.
>>> >If the simulations would be numerical reproducible, one should get the
>>> >same results. As they are not, the results will differ somewhat (would
>>> >think the more, the longer you simulate). But two different simulations
>>> >would be more equal to each other, than two simulations which start with
>>> >different velocity distributions for the particles.
>>> >
>>> >
>>> >If you're interested in an stochastic analysis of your system (meaning
>>> >simulations which are not equal - performing many pulling experiments in
>>> >reality, one would also have many different starting points) you could
>>> do
>>> >two things:
>>> >1) Run a look npt simulation, and use different frames to start the SMD
>>> >simulations. From each frame the particles should have a different
>>> velocity
>>> >distribution and the results of the SMD simulations should also differ.
>>> >(Depending on how many SMD simulations you want to perform, this might
>>> get
>>> >expensive, since the starting frame for SMD should be separated by more
>>> >then a few ps.)
>>> >2) Dump the 'npt.cpt' file and randomly determine new velocities for
>>> each
>>> >particle at the start of each SMD simulation. Since each simulation has
>>> a
>>> >different velocity distribution, the SMD simulation wont be the same.
>>> This
>>> >approach has only one weak point. Due to assigning new random velocities
>>> >you destroy the thermal equilibrium of the system. But if the system was
>>> >well equilibrated before, this distrubance should only be small and
>>> after
>>> >the first 100-200 ps of the SMD simulaton the system is in thermal
>>> >equilibrium. If the complete SMD simulation is much longer (couple of
>>> ns),
>>> >the interesting stuff would happen longer after the inital simulation
>>> time
>>> >with the destroyed equilibrium.
>>> >
>>> >Hope this helps
>>> >Thomas
>>> >
>>> >
>>> >
>>> >Am 26.04.2013 12:00, 
>>> >schriebgmx-users-request@**gromacs.org
>>> :
>>> >
>>> >Dear Users,
>>>
 >>
 >>I am running my puling simulations of ligand with constant velocity.
 First
 >>I minimize and equilibrate my system:
 >>
 >>grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
 >>mdrun -s em.tpr -deffnm em
 >>grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o
 nvt298.tpr
 >>mdrun -s nvt298.tpr -deffnm nvt298
 >>grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
 >>topol.top -o npt298.tpr
 >>mdrun -s npt298.tpr -deffnm npt298
 >>
 >>Then I run 10 pulling simulations with the same mdp file:
 >>
 >>grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t
 npt298.cpt
 >>-o
 >>pull_1.tpr
 >>mpiexec mdrun -s pull_1.tpr -deffnm pull_1
 >>
 >>...
 >>
 >>grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t
 npt298.cpt
 >>-o
 >>pull_10.tpr
 >>mpiexec mdrun -s pull_10.tpr -deffnm pull_10
 >>
 >>
 >>I get 3 different (but similar) profiles (Force vs time) with 10
 >>simulations as some of them produce exactly the same results... In
 another
 >>system with the same methodology I get 10 similar but different
 profiles.
 >>I
 >>am wondering why in this case only 3 types are possible... Shall I try
 >>grompp without -t npt.cpt ?
 >>
 >>Steven
 >>

>>>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.

[gmx-users] Re: SMD - reproducibility

[Thomas Schlesier]

Don't know. One idea i have: Take a flexible and a relative rigid system 
and perform simulations with the same starting conditions (-> using -t 
*.cpt). I would imagine that for the flexible system the trajectories 
start earlier to deviate, since more stuff could happen (system is more 
flexible -> greater configurational space). For the rigid system the 
configurational space is smaller, so the probability is higher to always 
follow the same trajectory if one starts with a predefinded velocity and 
direction.
But don't know if this is true, but it's the first thing which comes to 
my mind.



Am 26.04.2013 14:01, schrieb gmx-users-requ...@gromacs.org:

Thanks for this. I think option 2 is more reasonable. However, still do not
know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD
simulations...

On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesierwrote:


>Think i now understand your question. Forget what i wrote before.
>I could imagine the the 'grompp -t npt.cpt' part is a problem.
>If the simulations would be numerical reproducible, one should get the
>same results. As they are not, the results will differ somewhat (would
>think the more, the longer you simulate). But two different simulations
>would be more equal to each other, than two simulations which start with
>different velocity distributions for the particles.
>
>
>If you're interested in an stochastic analysis of your system (meaning
>simulations which are not equal - performing many pulling experiments in
>reality, one would also have many different starting points) you could do
>two things:
>1) Run a look npt simulation, and use different frames to start the SMD
>simulations. From each frame the particles should have a different velocity
>distribution and the results of the SMD simulations should also differ.
>(Depending on how many SMD simulations you want to perform, this might get
>expensive, since the starting frame for SMD should be separated by more
>then a few ps.)
>2) Dump the 'npt.cpt' file and randomly determine new velocities for each
>particle at the start of each SMD simulation. Since each simulation has a
>different velocity distribution, the SMD simulation wont be the same. This
>approach has only one weak point. Due to assigning new random velocities
>you destroy the thermal equilibrium of the system. But if the system was
>well equilibrated before, this distrubance should only be small and after
>the first 100-200 ps of the SMD simulaton the system is in thermal
>equilibrium. If the complete SMD simulation is much longer (couple of ns),
>the interesting stuff would happen longer after the inital simulation time
>with the destroyed equilibrium.
>
>Hope this helps
>Thomas
>
>
>
>Am 26.04.2013 12:00, schriebgmx-users-requ...@gromacs.org:
>
>Dear Users,

>>
>>I am running my puling simulations of ligand with constant velocity. First
>>I minimize and equilibrate my system:
>>
>>grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
>>mdrun -s em.tpr -deffnm em
>>grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr
>>mdrun -s nvt298.tpr -deffnm nvt298
>>grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
>>topol.top -o npt298.tpr
>>mdrun -s npt298.tpr -deffnm npt298
>>
>>Then I run 10 pulling simulations with the same mdp file:
>>
>>grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt
>>-o
>>pull_1.tpr
>>mpiexec mdrun -s pull_1.tpr -deffnm pull_1
>>
>>...
>>
>>grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt
>>-o
>>pull_10.tpr
>>mpiexec mdrun -s pull_10.tpr -deffnm pull_10
>>
>>
>>I get 3 different (but similar) profiles (Force vs time) with 10
>>simulations as some of them produce exactly the same results... In another
>>system with the same methodology I get 10 similar but different profiles.
>>I
>>am wondering why in this case only 3 types are possible... Shall I try
>>grompp without -t npt.cpt ?
>>
>>Steven
>>


--
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Re: [gmx-users] Re: SMD - reproducibility

[Steven Neumann]

Thanks for this. I think option 2 is more reasonable. However, still do not
know why I get sometimes 3 types of profiels and sometimes 10 for 10 SMD
simulations...

On Fri, Apr 26, 2013 at 12:46 PM, Thomas Schlesier wrote:

> Think i now understand your question. Forget what i wrote before.
> I could imagine the the 'grompp -t npt.cpt' part is a problem.
> If the simulations would be numerical reproducible, one should get the
> same results. As they are not, the results will differ somewhat (would
> think the more, the longer you simulate). But two different simulations
> would be more equal to each other, than two simulations which start with
> different velocity distributions for the particles.
>
>
> If you're interested in an stochastic analysis of your system (meaning
> simulations which are not equal - performing many pulling experiments in
> reality, one would also have many different starting points) you could do
> two things:
> 1) Run a look npt simulation, and use different frames to start the SMD
> simulations. From each frame the particles should have a different velocity
> distribution and the results of the SMD simulations should also differ.
> (Depending on how many SMD simulations you want to perform, this might get
> expensive, since the starting frame for SMD should be separated by more
> then a few ps.)
> 2) Dump the 'npt.cpt' file and randomly determine new velocities for each
> particle at the start of each SMD simulation. Since each simulation has a
> different velocity distribution, the SMD simulation wont be the same. This
> approach has only one weak point. Due to assigning new random velocities
> you destroy the thermal equilibrium of the system. But if the system was
> well equilibrated before, this distrubance should only be small and after
> the first 100-200 ps of the SMD simulaton the system is in thermal
> equilibrium. If the complete SMD simulation is much longer (couple of ns),
> the interesting stuff would happen longer after the inital simulation time
> with the destroyed equilibrium.
>
> Hope this helps
> Thomas
>
>
>
> Am 26.04.2013 12:00, schrieb gmx-users-requ...@gromacs.org:
>
> Dear Users,
>>
>> I am running my puling simulations of ligand with constant velocity. First
>> I minimize and equilibrate my system:
>>
>> grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
>> mdrun -s em.tpr -deffnm em
>> grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr
>> mdrun -s nvt298.tpr -deffnm nvt298
>> grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
>> topol.top -o npt298.tpr
>> mdrun -s npt298.tpr -deffnm npt298
>>
>> Then I run 10 pulling simulations with the same mdp file:
>>
>> grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt
>> -o
>> pull_1.tpr
>> mpiexec mdrun -s pull_1.tpr -deffnm pull_1
>>
>> ...
>>
>> grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt
>> -o
>> pull_10.tpr
>> mpiexec mdrun -s pull_10.tpr -deffnm pull_10
>>
>>
>> I get 3 different (but similar) profiles (Force vs time) with 10
>> simulations as some of them produce exactly the same results... In another
>> system with the same methodology I get 10 similar but different profiles.
>> I
>> am wondering why in this case only 3 types are possible... Shall I try
>> grompp without -t npt.cpt ?
>>
>> Steven
>>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
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* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: SMD - reproducibility

[Thomas Schlesier]

Think i now understand your question. Forget what i wrote before.
I could imagine the the 'grompp -t npt.cpt' part is a problem.
If the simulations would be numerical reproducible, one should get the 
same results. As they are not, the results will differ somewhat (would 
think the more, the longer you simulate). But two different simulations 
would be more equal to each other, than two simulations which start with 
different velocity distributions for the particles.



If you're interested in an stochastic analysis of your system (meaning 
simulations which are not equal - performing many pulling experiments in 
reality, one would also have many different starting points) you could 
do two things:
1) Run a look npt simulation, and use different frames to start the SMD 
simulations. From each frame the particles should have a different 
velocity distribution and the results of the SMD simulations should also 
differ. (Depending on how many SMD simulations you want to perform, this 
might get expensive, since the starting frame for SMD should be 
separated by more then a few ps.)
2) Dump the 'npt.cpt' file and randomly determine new velocities for 
each particle at the start of each SMD simulation. Since each simulation 
has a different velocity distribution, the SMD simulation wont be the 
same. This approach has only one weak point. Due to assigning new random 
velocities you destroy the thermal equilibrium of the system. But if the 
system was well equilibrated before, this distrubance should only be 
small and after the first 100-200 ps of the SMD simulaton the system is 
in thermal equilibrium. If the complete SMD simulation is much longer 
(couple of ns), the interesting stuff would happen longer after the 
inital simulation time with the destroyed equilibrium.


Hope this helps
Thomas



Am 26.04.2013 12:00, schrieb gmx-users-requ...@gromacs.org:

Dear Users,

I am running my puling simulations of ligand with constant velocity. First
I minimize and equilibrate my system:

grompp -f minim.mdp -c Solvions.gro -p topol.top -o em.tpr
mdrun -s em.tpr -deffnm em
grompp -f nvt298US.mdp -n index.ndx -c em.gro -p topol.top -o nvt298.tpr
mdrun -s nvt298.tpr -deffnm nvt298
grompp -f npt298US.mdp -n index.ndx -c nvt298.gro -t nvt298.cpt -p
topol.top -o npt298.tpr
mdrun -s npt298.tpr -deffnm npt298

Then I run 10 pulling simulations with the same mdp file:

grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o
pull_1.tpr
mpiexec mdrun -s pull_1.tpr -deffnm pull_1

...

grompp -f pull.mdp -c npt298.gro -p topol.top -n index.ndx -t npt298.cpt -o
pull_10.tpr
mpiexec mdrun -s pull_10.tpr -deffnm pull_10


I get 3 different (but similar) profiles (Force vs time) with 10
simulations as some of them produce exactly the same results... In another
system with the same methodology I get 10 similar but different profiles. I
am wondering why in this case only 3 types are possible... Shall I try
grompp without -t npt.cpt ?

Steven


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