Re: [gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep

[Sudip Das]

Hi Peter,

Sorry for the delay. According to your suggestion, I have equilibrated my
system with gradually increasing time step (1, 2, 5, 10, 15, 20 fs). After
that, the production step is running successfully.

Thanks a lot for your kind help!

Best regards,
Sudip

On Thu, Jun 29, 2017 at 2:32 PM, Peter Kroon  wrote:

> Hi Sudip,
>
>
> we had a short discussion over coffee. We also get these warnings, but
> they don't generally lead to significant instabilities. This means you
> probably have an equilibration issue. Could you try equilibrating your
> system with increasing timesteps? So first equilibrate with 5fs, then
> continue with 10 fs, 15fs and finally 20 fs.
>
> If that doesn't work, could you give a more detailed description of your
> system?
>
>
> Peter
>
>
> On 29-06-17 10:07, Peter Kroon wrote:
> > Hi Sudip,
> >
> >
> > there's a dedicated forum for these Martini questions on cgmartini.nl.
> > Recently there was a similar question there
> > (http://cgmartini.nl/index.php/component/kunena/7-mdp-
> options/5491-gpu-verlet-oscillational-period#7308).
> >
> > To summarize, the bonds between the backbone beads are extremely stiff.
> > If your protein is small/short enough you can change them to
> > constraints. I'll start a discussion in the group here on how to handle
> > it further.
> >
> >
> > Peter
> >
> >
> > On 29-06-17 09:06, Sudip Das wrote:
> >> Dear All,
> >>
> >> I am running a CGMD simulation of protein and surfactant in water with
> >> Martini2.0 force field for surfactant and water and ELNEDYN2.2 force
> field
> >> for protein.
> >>
> >> The system is running fine with 20 fs integration timestep. But it
> leads to
> >> solid phase of water. So, I have introduce antifreeze water beads (which
> >> are 10% in number w.r.t. the total number of water beads). But after
> this,
> >> simulation is not at all running with 20 fs timestep and gives the
> error:
> >>
> >> segmentation fault (signal 11)
> >>
> >> Within output file, it shows:
> >>
> >> Step 2, time 0.04 (ps)  LINCS WARNING
> >> relative constraint deviation after LINCS:
> >> rms 0.007237, max 0.028381 (between atoms 20 and 21)
> >> bonds that rotated more than 30 degrees:
> >>  atom 1 atom 2  angle  previous, current, constraint length
> >>  20 21   30.40.1981   0.1895  0.1950
> >>
> >>
> >> I have tried to solve it in several ways, i.e., decreasing the time
> steps
> >> (it is running fine with 2 fs), equilibrating the system properly,
> >> compiling and running in serial version of gromacs (to test whether the
> >> error comes due to domain decomposition during parallel run) etc. Even
> >> though, I am getting the same error.
> >>
> >> While compiling the job with grompp, I got the below warning:
> >>
> >> WARNING 1 [file system.top, line 18]:
> >>   The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an
> >>   estimated oscillational period of 9.7e-02 ps, which is less than 5
> times
> >>   the time step of 2.0e-02 ps.
> >>   Maybe you forgot to change the constraints mdp option.
> >>
> >> But, following the link
> >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-
> users/2014-May/089120.html
> >> , I have ignored this warning using -maxwarn flag. Probably this
> wouldn't
> >> be the cause for this error, as I got exactly the same warning for the
> >> system without antifreeze water beads.
> >>
> >>
> >> Please help me to solve this problem. I would be happy to share my
> files if
> >> needed.
> >>
> >> Thanks in advance!
> >>
> >> Best regards.
> >> Sudip
> >
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep

[Peter Kroon]

Hi Sudip,


we had a short discussion over coffee. We also get these warnings, but
they don't generally lead to significant instabilities. This means you
probably have an equilibration issue. Could you try equilibrating your
system with increasing timesteps? So first equilibrate with 5fs, then
continue with 10 fs, 15fs and finally 20 fs.

If that doesn't work, could you give a more detailed description of your
system?


Peter


On 29-06-17 10:07, Peter Kroon wrote:
> Hi Sudip,
>
>
> there's a dedicated forum for these Martini questions on cgmartini.nl.
> Recently there was a similar question there
> (http://cgmartini.nl/index.php/component/kunena/7-mdp-options/5491-gpu-verlet-oscillational-period#7308).
>
> To summarize, the bonds between the backbone beads are extremely stiff.
> If your protein is small/short enough you can change them to
> constraints. I'll start a discussion in the group here on how to handle
> it further.
>
>
> Peter
>
>
> On 29-06-17 09:06, Sudip Das wrote:
>> Dear All,
>>
>> I am running a CGMD simulation of protein and surfactant in water with
>> Martini2.0 force field for surfactant and water and ELNEDYN2.2 force field
>> for protein.
>>
>> The system is running fine with 20 fs integration timestep. But it leads to
>> solid phase of water. So, I have introduce antifreeze water beads (which
>> are 10% in number w.r.t. the total number of water beads). But after this,
>> simulation is not at all running with 20 fs timestep and gives the error:
>>
>> segmentation fault (signal 11)
>>
>> Within output file, it shows:
>>
>> Step 2, time 0.04 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.007237, max 0.028381 (between atoms 20 and 21)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>>  20 21   30.40.1981   0.1895  0.1950
>>
>>
>> I have tried to solve it in several ways, i.e., decreasing the time steps
>> (it is running fine with 2 fs), equilibrating the system properly,
>> compiling and running in serial version of gromacs (to test whether the
>> error comes due to domain decomposition during parallel run) etc. Even
>> though, I am getting the same error.
>>
>> While compiling the job with grompp, I got the below warning:
>>
>> WARNING 1 [file system.top, line 18]:
>>   The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an
>>   estimated oscillational period of 9.7e-02 ps, which is less than 5 times
>>   the time step of 2.0e-02 ps.
>>   Maybe you forgot to change the constraints mdp option.
>>
>> But, following the link
>> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-May/089120.html
>> , I have ignored this warning using -maxwarn flag. Probably this wouldn't
>> be the cause for this error, as I got exactly the same warning for the
>> system without antifreeze water beads.
>>
>>
>> Please help me to solve this problem. I would be happy to share my files if
>> needed.
>>
>> Thanks in advance!
>>
>> Best regards.
>> Sudip
>


-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep

[Peter Kroon]

Hi Sudip,


there's a dedicated forum for these Martini questions on cgmartini.nl.
Recently there was a similar question there
(http://cgmartini.nl/index.php/component/kunena/7-mdp-options/5491-gpu-verlet-oscillational-period#7308).

To summarize, the bonds between the backbone beads are extremely stiff.
If your protein is small/short enough you can change them to
constraints. I'll start a discussion in the group here on how to handle
it further.


Peter


On 29-06-17 09:06, Sudip Das wrote:
> Dear All,
>
> I am running a CGMD simulation of protein and surfactant in water with
> Martini2.0 force field for surfactant and water and ELNEDYN2.2 force field
> for protein.
>
> The system is running fine with 20 fs integration timestep. But it leads to
> solid phase of water. So, I have introduce antifreeze water beads (which
> are 10% in number w.r.t. the total number of water beads). But after this,
> simulation is not at all running with 20 fs timestep and gives the error:
>
> segmentation fault (signal 11)
>
> Within output file, it shows:
>
> Step 2, time 0.04 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.007237, max 0.028381 (between atoms 20 and 21)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>  20 21   30.40.1981   0.1895  0.1950
>
>
> I have tried to solve it in several ways, i.e., decreasing the time steps
> (it is running fine with 2 fs), equilibrating the system properly,
> compiling and running in serial version of gromacs (to test whether the
> error comes due to domain decomposition during parallel run) etc. Even
> though, I am getting the same error.
>
> While compiling the job with grompp, I got the below warning:
>
> WARNING 1 [file system.top, line 18]:
>   The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an
>   estimated oscillational period of 9.7e-02 ps, which is less than 5 times
>   the time step of 2.0e-02 ps.
>   Maybe you forgot to change the constraints mdp option.
>
> But, following the link
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-May/089120.html
> , I have ignored this warning using -maxwarn flag. Probably this wouldn't
> be the cause for this error, as I got exactly the same warning for the
> system without antifreeze water beads.
>
>
> Please help me to solve this problem. I would be happy to share my files if
> needed.
>
> Thanks in advance!
>
> Best regards.
> Sudip


-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep

[Sudip Das]

Dear All,

I am running a CGMD simulation of protein and surfactant in water with
Martini2.0 force field for surfactant and water and ELNEDYN2.2 force field
for protein.

The system is running fine with 20 fs integration timestep. But it leads to
solid phase of water. So, I have introduce antifreeze water beads (which
are 10% in number w.r.t. the total number of water beads). But after this,
simulation is not at all running with 20 fs timestep and gives the error:

segmentation fault (signal 11)

Within output file, it shows:

Step 2, time 0.04 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007237, max 0.028381 (between atoms 20 and 21)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 20 21   30.40.1981   0.1895  0.1950


I have tried to solve it in several ways, i.e., decreasing the time steps
(it is running fine with 2 fs), equilibrating the system properly,
compiling and running in serial version of gromacs (to test whether the
error comes due to domain decomposition during parallel run) etc. Even
though, I am getting the same error.

While compiling the job with grompp, I got the below warning:

WARNING 1 [file system.top, line 18]:
  The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an
  estimated oscillational period of 9.7e-02 ps, which is less than 5 times
  the time step of 2.0e-02 ps.
  Maybe you forgot to change the constraints mdp option.

But, following the link
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-May/089120.html
, I have ignored this warning using -maxwarn flag. Probably this wouldn't
be the cause for this error, as I got exactly the same warning for the
system without antifreeze water beads.


Please help me to solve this problem. I would be happy to share my files if
needed.

Thanks in advance!

Best regards.
Sudip
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.