Re: [gmx-users] Restarting crashed simmulation.

[Justin Lemkul]

On 5/11/18 2:11 PM, neelam wafa wrote:

Hi!
does this means that i should not have used -deffnm md_0_1 in the run
command? Actually I am a student and new to gromacs and have no experties
in it.  I think I need to read more about md run command options.


Use -deffnm, it saves you typing and makes your life easier, because 
instead of relying on generic, default file names, you know exactly what 
you did and what your files hold.


-Justin


Regards

On Fri, 11 May 2018 10:57 pm Mark Abraham,  wrote:


Hi,

Behaviour has changed since 5.1 to make it harder for this happen, but if
you do not call mdrun exactly the same way, older implementations of
checkpointing would try to be helpful and sometimes actually not be
helpful. This only happens if you try to over manage mdrun. It's best to
leave it alone to append with default file names, or use -noappend with
default filenames and get the part number added automatically. But if you
want to change the filenames to have a part number you manage yourself, you
have to manage everything else too...

Mark

On Fri, May 11, 2018 at 7:28 PM neelam wafa  wrote:


okay,

Thanks

On Fri, May 11, 2018 at 5:19 PM, Justin Lemkul  wrote:



On 5/11/18 1:18 PM, neelam wafa wrote:


*This is the message of gmx check for both the trajectories. I*t means
that
trajectory is not continuous. Am I right?


They are continuous (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc

starts

at the same time) and can be concatenated together. It appears your run

did

continue from the checkpoint file. I have no explanation for why the

file

names are not what one would expect.

-Justin

*gmx check -f md_0_1.xtc*

Checking file md_0_1.xtc
Reading frame   0 time0.000
# Atoms  67864
Precision 0.001 (nm)
Reading frame 200 time 2000.000


Item#frames Timestep (ps)
Step   27310
Time   27310
Lambda   0
Coords 27310
Velocities   0
Forces   0
Box27310

* gmx check -f traj_comp.xtc*


Checking file traj_comp.xtc
Reading frame   0 time 2720.000
# Atoms  67864
Precision 0.001 (nm)
Last frame 13 time 2850.000


Item#frames Timestep (ps)
Step1410
Time1410
Lambda   0
Coords  1410
Velocities   0
Forces   0
Box 1410


On Fri, May 11, 2018 at 5:12 PM, neelam wafa 
wrote:

The previous command was :

gmx mdrun -deffnm md_0_1

I didn't ust -cpi falg .

On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul 

wrote:



On 5/11/18 12:52 PM, neelam wafa wrote:

I used this command:

gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt

But I think its not appending as new files are being generated with
names
state.cpt, state_prev.cpt and traj_comp.xtc
while the previous files were md_0_1.cpt, md_0_1_prev.cpt and
md_0_1.xtc.
Why has it happened ? I have checked log files but not able to

infer

a

proper answer.

The file names are contained within the .cpt file, and those are

what

will be written. You haven't said what your previous command was,

but

the
use of -deffnm makes this much easier:

gmx mdrun -deffnm md_0_1 -cpi

You will always get clearly named files.

If its not appened, will the final trajectory .xtc obtained cover

the

whole
simmulation or I ll have to combine both results?

Use gmx check.

-Justin


Regards


On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul 
wrote:


On 5/11/18 10:42 AM, neelam wafa wrote:

Dear Sir Justin!


I have restarted the simmulation but its producing a separate log
file
starting from the step where restarted. Is it normal response or
there
is
some problem with my restart?

That shouldn't happen; everything should be appended unless there

was

some
problem (check the .log file itself and stdout/stderr for

messages).

Appending is for convenience but there is no functional

requirement

for
it
(I never append on the fly by personal preference, I just

concatenate

later).

-Justin


Thanks in advance.

On Fri, May 11, 2018 at 12:06 PM, neelam wafa <

neelam.w...@gmail.com>

wrote:

Thanks Sir Justin!

I have continued the simmulation from the last step.

Regards

On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul <

jalem...@vt.edu>

wrote:


On 5/10/18 7:08 AM, neelam wafa wrote:


Hi gmx users!

I am running a 5ns md simmulation of a protein with 250

steps.

It
crashed at  136 steps due to some power problem. Now I

want

to

continue
this simmulation. In the manual following command is given:

mdrun -s topol.tpr -cpi state.cpt

but I am confused which file is state.cpt. I have got two cpt
files
md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?

Look at the time stamps of the files and inspect their

contents

with

gmx

check. You will see an obvious difference in what they contain.
Also
consult the mdrun help info, which specifically addresses your
question.

Re: [gmx-users] Restarting crashed simmulation.

[neelam wafa]

Hi!
does this means that i should not have used -deffnm md_0_1 in the run
command? Actually I am a student and new to gromacs and have no experties
in it.  I think I need to read more about md run command options.

Regards

On Fri, 11 May 2018 10:57 pm Mark Abraham,  wrote:

> Hi,
>
> Behaviour has changed since 5.1 to make it harder for this happen, but if
> you do not call mdrun exactly the same way, older implementations of
> checkpointing would try to be helpful and sometimes actually not be
> helpful. This only happens if you try to over manage mdrun. It's best to
> leave it alone to append with default file names, or use -noappend with
> default filenames and get the part number added automatically. But if you
> want to change the filenames to have a part number you manage yourself, you
> have to manage everything else too...
>
> Mark
>
> On Fri, May 11, 2018 at 7:28 PM neelam wafa  wrote:
>
> > okay,
> >
> > Thanks
> >
> > On Fri, May 11, 2018 at 5:19 PM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 5/11/18 1:18 PM, neelam wafa wrote:
> > >
> > >> *This is the message of gmx check for both the trajectories. I*t means
> > >> that
> > >> trajectory is not continuous. Am I right?
> > >>
> > >
> > > They are continuous (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc
> > starts
> > > at the same time) and can be concatenated together. It appears your run
> > did
> > > continue from the checkpoint file. I have no explanation for why the
> file
> > > names are not what one would expect.
> > >
> > > -Justin
> > >
> > > *gmx check -f md_0_1.xtc*
> > >>
> > >> Checking file md_0_1.xtc
> > >> Reading frame   0 time0.000
> > >> # Atoms  67864
> > >> Precision 0.001 (nm)
> > >> Reading frame 200 time 2000.000
> > >>
> > >>
> > >> Item#frames Timestep (ps)
> > >> Step   27310
> > >> Time   27310
> > >> Lambda   0
> > >> Coords 27310
> > >> Velocities   0
> > >> Forces   0
> > >> Box27310
> > >>
> > >> * gmx check -f traj_comp.xtc*
> > >>
> > >>
> > >> Checking file traj_comp.xtc
> > >> Reading frame   0 time 2720.000
> > >> # Atoms  67864
> > >> Precision 0.001 (nm)
> > >> Last frame 13 time 2850.000
> > >>
> > >>
> > >> Item#frames Timestep (ps)
> > >> Step1410
> > >> Time1410
> > >> Lambda   0
> > >> Coords  1410
> > >> Velocities   0
> > >> Forces   0
> > >> Box 1410
> > >>
> > >>
> > >> On Fri, May 11, 2018 at 5:12 PM, neelam wafa 
> > >> wrote:
> > >>
> > >> The previous command was :
> > >>>
> > >>> gmx mdrun -deffnm md_0_1
> > >>>
> > >>> I didn't ust -cpi falg .
> > >>>
> > >>> On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul 
> > wrote:
> > >>>
> > >>>
> >  On 5/11/18 12:52 PM, neelam wafa wrote:
> > 
> >  I used this command:
> > > gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt
> > >
> > > But I think its not appending as new files are being generated with
> > > names
> > > state.cpt, state_prev.cpt and traj_comp.xtc
> > > while the previous files were md_0_1.cpt, md_0_1_prev.cpt and
> > > md_0_1.xtc.
> > > Why has it happened ? I have checked log files but not able to
> infer
> > a
> > > proper answer.
> > >
> > > The file names are contained within the .cpt file, and those are
> what
> >  will be written. You haven't said what your previous command was,
> but
> >  the
> >  use of -deffnm makes this much easier:
> > 
> >  gmx mdrun -deffnm md_0_1 -cpi
> > 
> >  You will always get clearly named files.
> > 
> >  If its not appened, will the final trajectory .xtc obtained cover
> the
> > 
> > > whole
> > > simmulation or I ll have to combine both results?
> > >
> > > Use gmx check.
> > 
> >  -Justin
> > 
> > 
> >  Regards
> > 
> > >
> > > On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul 
> > > wrote:
> > >
> > >
> > > On 5/11/18 10:42 AM, neelam wafa wrote:
> > >>
> > >> Dear Sir Justin!
> > >>
> > >>> I have restarted the simmulation but its producing a separate log
> > >>> file
> > >>> starting from the step where restarted. Is it normal response or
> > >>> there
> > >>> is
> > >>> some problem with my restart?
> > >>>
> > >>> That shouldn't happen; everything should be appended unless there
> > was
> > >>>
> > >> some
> > >> problem (check the .log file itself and stdout/stderr for
> messages).
> > >> Appending is for convenience but there is no functional
> requirement
> > >> for
> > >> it
> > >> (I never append on the fly by personal preference, I just
> > concatenate
> > >> later).
> > >>
> > >> -Justin
> > >>
> > >>
> > >> Thanks in advance.
> > 

Re: [gmx-users] Restarting crashed simmulation.

[Mark Abraham]

Hi,

Behaviour has changed since 5.1 to make it harder for this happen, but if
you do not call mdrun exactly the same way, older implementations of
checkpointing would try to be helpful and sometimes actually not be
helpful. This only happens if you try to over manage mdrun. It's best to
leave it alone to append with default file names, or use -noappend with
default filenames and get the part number added automatically. But if you
want to change the filenames to have a part number you manage yourself, you
have to manage everything else too...

Mark

On Fri, May 11, 2018 at 7:28 PM neelam wafa  wrote:

> okay,
>
> Thanks
>
> On Fri, May 11, 2018 at 5:19 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 5/11/18 1:18 PM, neelam wafa wrote:
> >
> >> *This is the message of gmx check for both the trajectories. I*t means
> >> that
> >> trajectory is not continuous. Am I right?
> >>
> >
> > They are continuous (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc
> starts
> > at the same time) and can be concatenated together. It appears your run
> did
> > continue from the checkpoint file. I have no explanation for why the file
> > names are not what one would expect.
> >
> > -Justin
> >
> > *gmx check -f md_0_1.xtc*
> >>
> >> Checking file md_0_1.xtc
> >> Reading frame   0 time0.000
> >> # Atoms  67864
> >> Precision 0.001 (nm)
> >> Reading frame 200 time 2000.000
> >>
> >>
> >> Item#frames Timestep (ps)
> >> Step   27310
> >> Time   27310
> >> Lambda   0
> >> Coords 27310
> >> Velocities   0
> >> Forces   0
> >> Box27310
> >>
> >> * gmx check -f traj_comp.xtc*
> >>
> >>
> >> Checking file traj_comp.xtc
> >> Reading frame   0 time 2720.000
> >> # Atoms  67864
> >> Precision 0.001 (nm)
> >> Last frame 13 time 2850.000
> >>
> >>
> >> Item#frames Timestep (ps)
> >> Step1410
> >> Time1410
> >> Lambda   0
> >> Coords  1410
> >> Velocities   0
> >> Forces   0
> >> Box 1410
> >>
> >>
> >> On Fri, May 11, 2018 at 5:12 PM, neelam wafa 
> >> wrote:
> >>
> >> The previous command was :
> >>>
> >>> gmx mdrun -deffnm md_0_1
> >>>
> >>> I didn't ust -cpi falg .
> >>>
> >>> On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul 
> wrote:
> >>>
> >>>
>  On 5/11/18 12:52 PM, neelam wafa wrote:
> 
>  I used this command:
> > gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt
> >
> > But I think its not appending as new files are being generated with
> > names
> > state.cpt, state_prev.cpt and traj_comp.xtc
> > while the previous files were md_0_1.cpt, md_0_1_prev.cpt and
> > md_0_1.xtc.
> > Why has it happened ? I have checked log files but not able to infer
> a
> > proper answer.
> >
> > The file names are contained within the .cpt file, and those are what
>  will be written. You haven't said what your previous command was, but
>  the
>  use of -deffnm makes this much easier:
> 
>  gmx mdrun -deffnm md_0_1 -cpi
> 
>  You will always get clearly named files.
> 
>  If its not appened, will the final trajectory .xtc obtained cover the
> 
> > whole
> > simmulation or I ll have to combine both results?
> >
> > Use gmx check.
> 
>  -Justin
> 
> 
>  Regards
> 
> >
> > On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul 
> > wrote:
> >
> >
> > On 5/11/18 10:42 AM, neelam wafa wrote:
> >>
> >> Dear Sir Justin!
> >>
> >>> I have restarted the simmulation but its producing a separate log
> >>> file
> >>> starting from the step where restarted. Is it normal response or
> >>> there
> >>> is
> >>> some problem with my restart?
> >>>
> >>> That shouldn't happen; everything should be appended unless there
> was
> >>>
> >> some
> >> problem (check the .log file itself and stdout/stderr for messages).
> >> Appending is for convenience but there is no functional requirement
> >> for
> >> it
> >> (I never append on the fly by personal preference, I just
> concatenate
> >> later).
> >>
> >> -Justin
> >>
> >>
> >> Thanks in advance.
> >>
> >> On Fri, May 11, 2018 at 12:06 PM, neelam wafa <
> neelam.w...@gmail.com>
> >>> wrote:
> >>>
> >>> Thanks Sir Justin!
> >>>
> >>> I have continued the simmulation from the last step.
> 
>  Regards
> 
>  On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul 
>  wrote:
> 
> 
>  On 5/10/18 7:08 AM, neelam wafa wrote:
> 
> > Hi gmx users!
> >
> > I am running a 5ns md simmulation of a protein with 250
> steps.
> >> It
> >> crashed at  136 steps due to some 

Re: [gmx-users] Restarting crashed simmulation.

[neelam wafa]

okay,

Thanks

On Fri, May 11, 2018 at 5:19 PM, Justin Lemkul  wrote:

>
>
> On 5/11/18 1:18 PM, neelam wafa wrote:
>
>> *This is the message of gmx check for both the trajectories. I*t means
>> that
>> trajectory is not continuous. Am I right?
>>
>
> They are continuous (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc starts
> at the same time) and can be concatenated together. It appears your run did
> continue from the checkpoint file. I have no explanation for why the file
> names are not what one would expect.
>
> -Justin
>
> *gmx check -f md_0_1.xtc*
>>
>> Checking file md_0_1.xtc
>> Reading frame   0 time0.000
>> # Atoms  67864
>> Precision 0.001 (nm)
>> Reading frame 200 time 2000.000
>>
>>
>> Item#frames Timestep (ps)
>> Step   27310
>> Time   27310
>> Lambda   0
>> Coords 27310
>> Velocities   0
>> Forces   0
>> Box27310
>>
>> * gmx check -f traj_comp.xtc*
>>
>>
>> Checking file traj_comp.xtc
>> Reading frame   0 time 2720.000
>> # Atoms  67864
>> Precision 0.001 (nm)
>> Last frame 13 time 2850.000
>>
>>
>> Item#frames Timestep (ps)
>> Step1410
>> Time1410
>> Lambda   0
>> Coords  1410
>> Velocities   0
>> Forces   0
>> Box 1410
>>
>>
>> On Fri, May 11, 2018 at 5:12 PM, neelam wafa 
>> wrote:
>>
>> The previous command was :
>>>
>>> gmx mdrun -deffnm md_0_1
>>>
>>> I didn't ust -cpi falg .
>>>
>>> On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul  wrote:
>>>
>>>
 On 5/11/18 12:52 PM, neelam wafa wrote:

 I used this command:
> gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt
>
> But I think its not appending as new files are being generated with
> names
> state.cpt, state_prev.cpt and traj_comp.xtc
> while the previous files were md_0_1.cpt, md_0_1_prev.cpt and
> md_0_1.xtc.
> Why has it happened ? I have checked log files but not able to infer a
> proper answer.
>
> The file names are contained within the .cpt file, and those are what
 will be written. You haven't said what your previous command was, but
 the
 use of -deffnm makes this much easier:

 gmx mdrun -deffnm md_0_1 -cpi

 You will always get clearly named files.

 If its not appened, will the final trajectory .xtc obtained cover the

> whole
> simmulation or I ll have to combine both results?
>
> Use gmx check.

 -Justin


 Regards

>
> On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul 
> wrote:
>
>
> On 5/11/18 10:42 AM, neelam wafa wrote:
>>
>> Dear Sir Justin!
>>
>>> I have restarted the simmulation but its producing a separate log
>>> file
>>> starting from the step where restarted. Is it normal response or
>>> there
>>> is
>>> some problem with my restart?
>>>
>>> That shouldn't happen; everything should be appended unless there was
>>>
>> some
>> problem (check the .log file itself and stdout/stderr for messages).
>> Appending is for convenience but there is no functional requirement
>> for
>> it
>> (I never append on the fly by personal preference, I just concatenate
>> later).
>>
>> -Justin
>>
>>
>> Thanks in advance.
>>
>> On Fri, May 11, 2018 at 12:06 PM, neelam wafa 
>>> wrote:
>>>
>>> Thanks Sir Justin!
>>>
>>> I have continued the simmulation from the last step.

 Regards

 On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul 
 wrote:


 On 5/10/18 7:08 AM, neelam wafa wrote:

> Hi gmx users!
>
> I am running a 5ns md simmulation of a protein with 250 steps.
>> It
>> crashed at  136 steps due to some power problem. Now I want to
>> continue
>> this simmulation. In the manual following command is given:
>>
>> mdrun -s topol.tpr -cpi state.cpt
>>
>> but I am confused which file is state.cpt. I have got two cpt
>> files
>> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?
>>
>> Look at the time stamps of the files and inspect their contents
>> with
>>
>> gmx
> check. You will see an obvious difference in what they contain.
> Also
> consult the mdrun help info, which specifically addresses your
> question.
>
> Also I did not get a md_1_0.gro file/ Is is due to incomplete
> simmulation?
> Yes, because that file is only produced from the last step.
>
> Also do I need to specify  -append flag or not? I am using version
> 5.1.5
> -append has been the 

Re: [gmx-users] Restarting crashed simmulation.

[Justin Lemkul]

On 5/11/18 1:18 PM, neelam wafa wrote:

*This is the message of gmx check for both the trajectories. I*t means that
trajectory is not continuous. Am I right?


They are continuous (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc 
starts at the same time) and can be concatenated together. It appears 
your run did continue from the checkpoint file. I have no explanation 
for why the file names are not what one would expect.


-Justin


*gmx check -f md_0_1.xtc*

Checking file md_0_1.xtc
Reading frame   0 time0.000
# Atoms  67864
Precision 0.001 (nm)
Reading frame 200 time 2000.000


Item#frames Timestep (ps)
Step   27310
Time   27310
Lambda   0
Coords 27310
Velocities   0
Forces   0
Box27310

* gmx check -f traj_comp.xtc*

Checking file traj_comp.xtc
Reading frame   0 time 2720.000
# Atoms  67864
Precision 0.001 (nm)
Last frame 13 time 2850.000


Item#frames Timestep (ps)
Step1410
Time1410
Lambda   0
Coords  1410
Velocities   0
Forces   0
Box 1410


On Fri, May 11, 2018 at 5:12 PM, neelam wafa  wrote:


The previous command was :

gmx mdrun -deffnm md_0_1

I didn't ust -cpi falg .

On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul  wrote:



On 5/11/18 12:52 PM, neelam wafa wrote:


I used this command:
gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt

But I think its not appending as new files are being generated with names
state.cpt, state_prev.cpt and traj_comp.xtc
while the previous files were md_0_1.cpt, md_0_1_prev.cpt and md_0_1.xtc.
Why has it happened ? I have checked log files but not able to infer a
proper answer.


The file names are contained within the .cpt file, and those are what
will be written. You haven't said what your previous command was, but the
use of -deffnm makes this much easier:

gmx mdrun -deffnm md_0_1 -cpi

You will always get clearly named files.

If its not appened, will the final trajectory .xtc obtained cover the

whole
simmulation or I ll have to combine both results?


Use gmx check.

-Justin


Regards


On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul  wrote:



On 5/11/18 10:42 AM, neelam wafa wrote:

Dear Sir Justin!

I have restarted the simmulation but its producing a separate log file
starting from the step where restarted. Is it normal response or there
is
some problem with my restart?

That shouldn't happen; everything should be appended unless there was

some
problem (check the .log file itself and stdout/stderr for messages).
Appending is for convenience but there is no functional requirement for
it
(I never append on the fly by personal preference, I just concatenate
later).

-Justin


Thanks in advance.


On Fri, May 11, 2018 at 12:06 PM, neelam wafa 
wrote:

Thanks Sir Justin!


I have continued the simmulation from the last step.

Regards

On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul 
wrote:


On 5/10/18 7:08 AM, neelam wafa wrote:

Hi gmx users!


I am running a 5ns md simmulation of a protein with 250 steps.
It
crashed at  136 steps due to some power problem. Now I want to
continue
this simmulation. In the manual following command is given:

mdrun -s topol.tpr -cpi state.cpt

but I am confused which file is state.cpt. I have got two cpt files
md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?

Look at the time stamps of the files and inspect their contents with


gmx
check. You will see an obvious difference in what they contain. Also
consult the mdrun help info, which specifically addresses your
question.

Also I did not get a md_1_0.gro file/ Is is due to incomplete
simmulation?
Yes, because that file is only produced from the last step.

Also do I need to specify  -append flag or not? I am using version
5.1.5
-append has been the default option for many years. Again, see the
mdrun
help description.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

Re: [gmx-users] Restarting crashed simmulation.

[neelam wafa]

*This is the message of gmx check for both the trajectories. I*t means that
trajectory is not continuous. Am I right?

*gmx check -f md_0_1.xtc*

Checking file md_0_1.xtc
Reading frame   0 time0.000
# Atoms  67864
Precision 0.001 (nm)
Reading frame 200 time 2000.000


Item#frames Timestep (ps)
Step   27310
Time   27310
Lambda   0
Coords 27310
Velocities   0
Forces   0
Box27310

* gmx check -f traj_comp.xtc*

Checking file traj_comp.xtc
Reading frame   0 time 2720.000
# Atoms  67864
Precision 0.001 (nm)
Last frame 13 time 2850.000


Item#frames Timestep (ps)
Step1410
Time1410
Lambda   0
Coords  1410
Velocities   0
Forces   0
Box 1410


On Fri, May 11, 2018 at 5:12 PM, neelam wafa  wrote:

> The previous command was :
>
> gmx mdrun -deffnm md_0_1
>
> I didn't ust -cpi falg .
>
> On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 5/11/18 12:52 PM, neelam wafa wrote:
>>
>>> I used this command:
>>> gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt
>>>
>>> But I think its not appending as new files are being generated with names
>>> state.cpt, state_prev.cpt and traj_comp.xtc
>>> while the previous files were md_0_1.cpt, md_0_1_prev.cpt and md_0_1.xtc.
>>> Why has it happened ? I have checked log files but not able to infer a
>>> proper answer.
>>>
>>
>> The file names are contained within the .cpt file, and those are what
>> will be written. You haven't said what your previous command was, but the
>> use of -deffnm makes this much easier:
>>
>> gmx mdrun -deffnm md_0_1 -cpi
>>
>> You will always get clearly named files.
>>
>> If its not appened, will the final trajectory .xtc obtained cover the
>>> whole
>>> simmulation or I ll have to combine both results?
>>>
>>
>> Use gmx check.
>>
>> -Justin
>>
>>
>> Regards
>>>
>>>
>>> On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul  wrote:
>>>
>>>
 On 5/11/18 10:42 AM, neelam wafa wrote:

 Dear Sir Justin!
>
> I have restarted the simmulation but its producing a separate log file
> starting from the step where restarted. Is it normal response or there
> is
> some problem with my restart?
>
> That shouldn't happen; everything should be appended unless there was
 some
 problem (check the .log file itself and stdout/stderr for messages).
 Appending is for convenience but there is no functional requirement for
 it
 (I never append on the fly by personal preference, I just concatenate
 later).

 -Justin


 Thanks in advance.

> On Fri, May 11, 2018 at 12:06 PM, neelam wafa 
> wrote:
>
> Thanks Sir Justin!
>
>> I have continued the simmulation from the last step.
>>
>> Regards
>>
>> On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul 
>> wrote:
>>
>>
>> On 5/10/18 7:08 AM, neelam wafa wrote:
>>>
>>> Hi gmx users!
>>>
 I am running a 5ns md simmulation of a protein with 250 steps.
 It
 crashed at  136 steps due to some power problem. Now I want to
 continue
 this simmulation. In the manual following command is given:

 mdrun -s topol.tpr -cpi state.cpt

 but I am confused which file is state.cpt. I have got two cpt files
 md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?

 Look at the time stamps of the files and inspect their contents with

>>> gmx
>>> check. You will see an obvious difference in what they contain. Also
>>> consult the mdrun help info, which specifically addresses your
>>> question.
>>>
>>> Also I did not get a md_1_0.gro file/ Is is due to incomplete
>>> simmulation?
>>> Yes, because that file is only produced from the last step.
>>>
>>> Also do I need to specify  -append flag or not? I am using version
>>> 5.1.5
>>> -append has been the default option for many years. Again, see the
>>> mdrun
>>> help description.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>>
>>> ==
>>>
>>> --
>>> 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 

Re: [gmx-users] Restarting crashed simmulation.

[Justin Lemkul]

On 5/11/18 1:12 PM, neelam wafa wrote:

The previous command was :

gmx mdrun -deffnm md_0_1

I didn't ust -cpi falg .


Then the only explanation I can think of for what you are observing is 
that somehow md_0_1.cpt was not accessible, causing mdrun to start over 
from t = 0 and write a new set of files (because -s md_0_1.tpr does not 
write files with names md_0_1.*, only -deffnm does). Your new .log file 
should clearly indicate what time it started from. If it's t=0, then 
your loading from .cpt failed and your run started over. With new file 
names, you shouldn't have lost anything and could try to restart again 
once you identify the source of the problem.


-Justin



On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul  wrote:



On 5/11/18 12:52 PM, neelam wafa wrote:


I used this command:
gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt

But I think its not appending as new files are being generated with names
state.cpt, state_prev.cpt and traj_comp.xtc
while the previous files were md_0_1.cpt, md_0_1_prev.cpt and md_0_1.xtc.
Why has it happened ? I have checked log files but not able to infer a
proper answer.


The file names are contained within the .cpt file, and those are what will
be written. You haven't said what your previous command was, but the use of
-deffnm makes this much easier:

gmx mdrun -deffnm md_0_1 -cpi

You will always get clearly named files.

If its not appened, will the final trajectory .xtc obtained cover the whole

simmulation or I ll have to combine both results?


Use gmx check.

-Justin


Regards


On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul  wrote:



On 5/11/18 10:42 AM, neelam wafa wrote:

Dear Sir Justin!

I have restarted the simmulation but its producing a separate log file
starting from the step where restarted. Is it normal response or there
is
some problem with my restart?

That shouldn't happen; everything should be appended unless there was

some
problem (check the .log file itself and stdout/stderr for messages).
Appending is for convenience but there is no functional requirement for
it
(I never append on the fly by personal preference, I just concatenate
later).

-Justin


Thanks in advance.


On Fri, May 11, 2018 at 12:06 PM, neelam wafa 
wrote:

Thanks Sir Justin!


I have continued the simmulation from the last step.

Regards

On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul 
wrote:


On 5/10/18 7:08 AM, neelam wafa wrote:

Hi gmx users!


I am running a 5ns md simmulation of a protein with 250 steps. It
crashed at  136 steps due to some power problem. Now I want to
continue
this simmulation. In the manual following command is given:

mdrun -s topol.tpr -cpi state.cpt

but I am confused which file is state.cpt. I have got two cpt files
md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?

Look at the time stamps of the files and inspect their contents with


gmx
check. You will see an obvious difference in what they contain. Also
consult the mdrun help info, which specifically addresses your
question.

Also I did not get a md_1_0.gro file/ Is is due to incomplete
simmulation?
Yes, because that file is only produced from the last step.

Also do I need to specify  -append flag or not? I am using version
5.1.5
-append has been the default option for many years. Again, see the
mdrun
help description.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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.


--

==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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.



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

Re: [gmx-users] Restarting crashed simmulation.

[neelam wafa]

The previous command was :

gmx mdrun -deffnm md_0_1

I didn't ust -cpi falg .

On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul  wrote:

>
>
> On 5/11/18 12:52 PM, neelam wafa wrote:
>
>> I used this command:
>> gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt
>>
>> But I think its not appending as new files are being generated with names
>> state.cpt, state_prev.cpt and traj_comp.xtc
>> while the previous files were md_0_1.cpt, md_0_1_prev.cpt and md_0_1.xtc.
>> Why has it happened ? I have checked log files but not able to infer a
>> proper answer.
>>
>
> The file names are contained within the .cpt file, and those are what will
> be written. You haven't said what your previous command was, but the use of
> -deffnm makes this much easier:
>
> gmx mdrun -deffnm md_0_1 -cpi
>
> You will always get clearly named files.
>
> If its not appened, will the final trajectory .xtc obtained cover the whole
>> simmulation or I ll have to combine both results?
>>
>
> Use gmx check.
>
> -Justin
>
>
> Regards
>>
>>
>> On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul  wrote:
>>
>>
>>> On 5/11/18 10:42 AM, neelam wafa wrote:
>>>
>>> Dear Sir Justin!

 I have restarted the simmulation but its producing a separate log file
 starting from the step where restarted. Is it normal response or there
 is
 some problem with my restart?

 That shouldn't happen; everything should be appended unless there was
>>> some
>>> problem (check the .log file itself and stdout/stderr for messages).
>>> Appending is for convenience but there is no functional requirement for
>>> it
>>> (I never append on the fly by personal preference, I just concatenate
>>> later).
>>>
>>> -Justin
>>>
>>>
>>> Thanks in advance.
>>>
 On Fri, May 11, 2018 at 12:06 PM, neelam wafa 
 wrote:

 Thanks Sir Justin!

> I have continued the simmulation from the last step.
>
> Regards
>
> On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul 
> wrote:
>
>
> On 5/10/18 7:08 AM, neelam wafa wrote:
>>
>> Hi gmx users!
>>
>>> I am running a 5ns md simmulation of a protein with 250 steps. It
>>> crashed at  136 steps due to some power problem. Now I want to
>>> continue
>>> this simmulation. In the manual following command is given:
>>>
>>> mdrun -s topol.tpr -cpi state.cpt
>>>
>>> but I am confused which file is state.cpt. I have got two cpt files
>>> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?
>>>
>>> Look at the time stamps of the files and inspect their contents with
>>>
>> gmx
>> check. You will see an obvious difference in what they contain. Also
>> consult the mdrun help info, which specifically addresses your
>> question.
>>
>> Also I did not get a md_1_0.gro file/ Is is due to incomplete
>> simmulation?
>> Yes, because that file is only produced from the last step.
>>
>> Also do I need to specify  -append flag or not? I am using version
>> 5.1.5
>> -append has been the default option for many years. Again, see the
>> mdrun
>> help description.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalem...@vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==
>>
>> --
>> 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.
>>
>>
>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>>
>>> ==
>>>
>>> --
>>> 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.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> 

Re: [gmx-users] Restarting crashed simmulation.

[Justin Lemkul]

On 5/11/18 12:52 PM, neelam wafa wrote:

I used this command:
gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt

But I think its not appending as new files are being generated with names
state.cpt, state_prev.cpt and traj_comp.xtc
while the previous files were md_0_1.cpt, md_0_1_prev.cpt and md_0_1.xtc.
Why has it happened ? I have checked log files but not able to infer a
proper answer.


The file names are contained within the .cpt file, and those are what 
will be written. You haven't said what your previous command was, but 
the use of -deffnm makes this much easier:


gmx mdrun -deffnm md_0_1 -cpi

You will always get clearly named files.


If its not appened, will the final trajectory .xtc obtained cover the whole
simmulation or I ll have to combine both results?


Use gmx check.

-Justin


Regards


On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul  wrote:



On 5/11/18 10:42 AM, neelam wafa wrote:


Dear Sir Justin!

I have restarted the simmulation but its producing a separate log file
starting from the step where restarted. Is it normal response or there is
some problem with my restart?


That shouldn't happen; everything should be appended unless there was some
problem (check the .log file itself and stdout/stderr for messages).
Appending is for convenience but there is no functional requirement for it
(I never append on the fly by personal preference, I just concatenate
later).

-Justin


Thanks in advance.

On Fri, May 11, 2018 at 12:06 PM, neelam wafa 
wrote:

Thanks Sir Justin!

I have continued the simmulation from the last step.

Regards

On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul  wrote:



On 5/10/18 7:08 AM, neelam wafa wrote:

Hi gmx users!

I am running a 5ns md simmulation of a protein with 250 steps. It
crashed at  136 steps due to some power problem. Now I want to
continue
this simmulation. In the manual following command is given:

mdrun -s topol.tpr -cpi state.cpt

but I am confused which file is state.cpt. I have got two cpt files
md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?

Look at the time stamps of the files and inspect their contents with

gmx
check. You will see an obvious difference in what they contain. Also
consult the mdrun help info, which specifically addresses your question.

Also I did not get a md_1_0.gro file/ Is is due to incomplete
simmulation?
Yes, because that file is only produced from the last step.

Also do I need to specify  -append flag or not? I am using version 5.1.5
-append has been the default option for many years. Again, see the mdrun
help description.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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.



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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.



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

--
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] Restarting crashed simmulation.

[neelam wafa]

I used this command:
gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt

But I think its not appending as new files are being generated with names
state.cpt, state_prev.cpt and traj_comp.xtc
while the previous files were md_0_1.cpt, md_0_1_prev.cpt and md_0_1.xtc.
Why has it happened ? I have checked log files but not able to infer a
proper answer.
If its not appened, will the final trajectory .xtc obtained cover the whole
simmulation or I ll have to combine both results?

Regards


On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul  wrote:

>
>
> On 5/11/18 10:42 AM, neelam wafa wrote:
>
>> Dear Sir Justin!
>>
>> I have restarted the simmulation but its producing a separate log file
>> starting from the step where restarted. Is it normal response or there is
>> some problem with my restart?
>>
>
> That shouldn't happen; everything should be appended unless there was some
> problem (check the .log file itself and stdout/stderr for messages).
> Appending is for convenience but there is no functional requirement for it
> (I never append on the fly by personal preference, I just concatenate
> later).
>
> -Justin
>
>
> Thanks in advance.
>>
>> On Fri, May 11, 2018 at 12:06 PM, neelam wafa 
>> wrote:
>>
>> Thanks Sir Justin!
>>> I have continued the simmulation from the last step.
>>>
>>> Regards
>>>
>>> On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul  wrote:
>>>
>>>
 On 5/10/18 7:08 AM, neelam wafa wrote:

 Hi gmx users!
>
> I am running a 5ns md simmulation of a protein with 250 steps. It
> crashed at  136 steps due to some power problem. Now I want to
> continue
> this simmulation. In the manual following command is given:
>
> mdrun -s topol.tpr -cpi state.cpt
>
> but I am confused which file is state.cpt. I have got two cpt files
> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?
>
> Look at the time stamps of the files and inspect their contents with
 gmx
 check. You will see an obvious difference in what they contain. Also
 consult the mdrun help info, which specifically addresses your question.

 Also I did not get a md_1_0.gro file/ Is is due to incomplete
 simmulation?
 Yes, because that file is only produced from the last step.

 Also do I need to specify  -append flag or not? I am using version 5.1.5
 -append has been the default option for many years. Again, see the mdrun
 help description.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Assistant Professor
 Virginia Tech Department of Biochemistry

 303 Engel Hall
 340 West Campus Dr.
 Blacksburg, VA 24061

 jalem...@vt.edu | (540) 231-3129
 http://www.thelemkullab.com

 ==

 --
 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.


>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> 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!

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Distribution of water polarization

[rose rahmani]

On Fri, 11 May 2018, 20:04 Justin Lemkul,  wrote:

>
>
> On 5/11/18 11:29 AM, rose rahmani wrote:
> > On Fri, 11 May 2018, 19:38 Justin Lemkul,  wrote:
> >
> >>
> >> On 5/11/18 11:06 AM, rose rahmani wrote:
> >>> Hi,
> >>>
> >>> How can i calculate the distribution of water polarization for example
> >> for
> >>> the first two layers of water at the solid surface?
> >>>
> >>> How about the number of water molecules with a given polarization?
> >>>
> >>> I mean exactly figure2 of this article.
> >>> Can gmx dipoles do it?
> >> Did you do a polarizable simulation?
> >>
> > No, it is sth like calculating the distribution of polarization (dipole)
> in
> > different dimensions separately. Sth like different orientation of water
> > molecules which cause to different orientations of dipoles in different
> > dimensions. (Hope to explain clearly, if it's possible please take a look
> > at the article)
>
> There is no article, nothing linked, but in

Sorry, i forgot to send it. The figure 2

https://aip.scitation.org/doi/abs/10.1063/1.4866763?journalCode=jcp

any case I'm not going to
> have time to look into it.
>
Ok, but i sent... It maybe useful for someone. ;)

> If you've done a classical, nonpolarizable MD simulation, you can make
> no claims about polarization. You could compute properties related to
> water molecule orientation (e.g. gmx hydorder), which will tell you
> about the dipole moment orientation in the context of a fixed triangle
> of charges, but that's all you're going to get from simulations like
> these. FWIW, in reality, the dipole moment of the water molecules will
> not be exactly related to these fixed geometries, so this is a weak
> comparison, in my mind.
>
Thank you so much for your detailed answer.

> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] Distribution of water polarization

[Justin Lemkul]

On 5/11/18 11:29 AM, rose rahmani wrote:

On Fri, 11 May 2018, 19:38 Justin Lemkul,  wrote:



On 5/11/18 11:06 AM, rose rahmani wrote:

Hi,

How can i calculate the distribution of water polarization for example

for

the first two layers of water at the solid surface?

How about the number of water molecules with a given polarization?

I mean exactly figure2 of this article.
Can gmx dipoles do it?

Did you do a polarizable simulation?


No, it is sth like calculating the distribution of polarization (dipole) in
different dimensions separately. Sth like different orientation of water
molecules which cause to different orientations of dipoles in different
dimensions. (Hope to explain clearly, if it's possible please take a look
at the article)


There is no article, nothing linked, but in any case I'm not going to 
have time to look into it.


If you've done a classical, nonpolarizable MD simulation, you can make 
no claims about polarization. You could compute properties related to 
water molecule orientation (e.g. gmx hydorder), which will tell you 
about the dipole moment orientation in the context of a fixed triangle 
of charges, but that's all you're going to get from simulations like 
these. FWIW, in reality, the dipole moment of the water molecules will 
not be exactly related to these fixed geometries, so this is a weak 
comparison, in my mind.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] Distribution of water polarization

[rose rahmani]

On Fri, 11 May 2018, 19:38 Justin Lemkul,  wrote:

>
>
> On 5/11/18 11:06 AM, rose rahmani wrote:
> > Hi,
> >
> > How can i calculate the distribution of water polarization for example
> for
> > the first two layers of water at the solid surface?
> >
> > How about the number of water molecules with a given polarization?
> >
> > I mean exactly figure2 of this article.
> > Can gmx dipoles do it?
>
> Did you do a polarizable simulation?
>
No, it is sth like calculating the distribution of polarization (dipole) in
different dimensions separately. Sth like different orientation of water
molecules which cause to different orientations of dipoles in different
dimensions. (Hope to explain clearly, if it's possible please take a look
at the article)

> Rigid, fixed-charge water molecules all have identical dipole moments,
> by definition.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
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> * Please search the archive at
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Re: [gmx-users] Distribution of water polarization

[Justin Lemkul]

On 5/11/18 11:06 AM, rose rahmani wrote:

Hi,

How can i calculate the distribution of water polarization for example for
the first two layers of water at the solid surface?

How about the number of water molecules with a given polarization?

I mean exactly figure2 of this article.
Can gmx dipoles do it?


Did you do a polarizable simulation?

Rigid, fixed-charge water molecules all have identical dipole moments, 
by definition.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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[gmx-users] Distribution of water polarization

[rose rahmani]

Hi,

How can i calculate the distribution of water polarization for example for
the first two layers of water at the solid surface?

How about the number of water molecules with a given polarization?

I mean exactly figure2 of this article.
Can gmx dipoles do it?


Best regards
-Rose
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Re: [gmx-users] Restarting crashed simmulation.

[Justin Lemkul]

On 5/11/18 10:42 AM, neelam wafa wrote:

Dear Sir Justin!

I have restarted the simmulation but its producing a separate log file
starting from the step where restarted. Is it normal response or there is
some problem with my restart?


That shouldn't happen; everything should be appended unless there was 
some problem (check the .log file itself and stdout/stderr for 
messages). Appending is for convenience but there is no functional 
requirement for it (I never append on the fly by personal preference, I 
just concatenate later).


-Justin


Thanks in advance.

On Fri, May 11, 2018 at 12:06 PM, neelam wafa  wrote:


Thanks Sir Justin!
I have continued the simmulation from the last step.

Regards

On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul  wrote:



On 5/10/18 7:08 AM, neelam wafa wrote:


Hi gmx users!

I am running a 5ns md simmulation of a protein with 250 steps. It
crashed at  136 steps due to some power problem. Now I want to
continue
this simmulation. In the manual following command is given:

mdrun -s topol.tpr -cpi state.cpt

but I am confused which file is state.cpt. I have got two cpt files
md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?


Look at the time stamps of the files and inspect their contents with gmx
check. You will see an obvious difference in what they contain. Also
consult the mdrun help info, which specifically addresses your question.

Also I did not get a md_1_0.gro file/ Is is due to incomplete simmulation?
Yes, because that file is only produced from the last step.

Also do I need to specify  -append flag or not? I am using version 5.1.5
-append has been the default option for many years. Again, see the mdrun
help description.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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Re: [gmx-users] V2018.1 building issues

[kevin chen]

Ok, got it, thanks!

On Fri, May 11, 2018 at 10:23 AM, Mark Abraham 
wrote:

> Hi,
>
> I'm surprised that was able to work in 2016, but nevertheless it was never
> designed to work and should not be relied upon. Build a separate binary for
> each hardware flavor and have the module system choose the correct one to
> load, per our installation guide
> http://manual.gromacs.org/documentation/2018/install-
> guide/index.html#portability-aspects
>
>
> Mark
>
> On Thu, May 10, 2018 at 4:17 PM kevin chen  wrote:
>
> > Hi  Gromacs Users,
> >
> > I'm having this weird issue while trying to build the new V2018.1 on
> > Stampede2, which has both SKX amd KNL nodes on it. For V2016 and older,
> in
> > order to run the same executable(mdrun_mpi), we have to build the "fat"
> > binary with " -DGMX_SIMD=AVX_512" and "-DCMAKE_C_FLAGS="-O3 -xCORE-AVX2
> > -axCORE-AVX512,MIC-AVX512 ". That actually worked just fine for V2016. We
> > can actually run simulation on both skx and knl without any issues using
> > the same binary. However, for some reason the same trick no longer works
> > with V2018.1. We tried to build V2018.1 with the exactly same building
> > script with " -DGMX_SIMD=AVX_512" option applied. This time around the
> > binary(mdrun_mpi) only works on skx node but no on knls. So I was
> wondering
> > is there any thing change since V2016 causing this issue or am I missing
> > anything here? Thanks advanced for any pointers you guys might provide.
> >
> > Our building environment,
> >
> > Currently Loaded Modules:
> >   1) intel/17.0.4   3) git/2.9.0   5) python/2.7.13   7) TACC
> >   2) impi/17.0.34) autotools/1.1   6) xalt/1.7.7  8) cmake/3.10.2
> >
> > Best,
> >
> > Kevin
> > --
> > Gromacs Users mailing list
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> > posting!
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Re: [gmx-users] Restarting crashed simmulation.

[neelam wafa]

Dear Sir Justin!

I have restarted the simmulation but its producing a separate log file
starting from the step where restarted. Is it normal response or there is
some problem with my restart?

Thanks in advance.

On Fri, May 11, 2018 at 12:06 PM, neelam wafa  wrote:

> Thanks Sir Justin!
> I have continued the simmulation from the last step.
>
> Regards
>
> On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 5/10/18 7:08 AM, neelam wafa wrote:
>>
>>> Hi gmx users!
>>>
>>> I am running a 5ns md simmulation of a protein with 250 steps. It
>>> crashed at  136 steps due to some power problem. Now I want to
>>> continue
>>> this simmulation. In the manual following command is given:
>>>
>>> mdrun -s topol.tpr -cpi state.cpt
>>>
>>> but I am confused which file is state.cpt. I have got two cpt files
>>> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?
>>>
>>
>> Look at the time stamps of the files and inspect their contents with gmx
>> check. You will see an obvious difference in what they contain. Also
>> consult the mdrun help info, which specifically addresses your question.
>>
>> Also I did not get a md_1_0.gro file/ Is is due to incomplete simmulation?
>>>
>>
>> Yes, because that file is only produced from the last step.
>>
>> Also do I need to specify  -append flag or not? I am using version 5.1.5
>>>
>>
>> -append has been the default option for many years. Again, see the mdrun
>> help description.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalem...@vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
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>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] Bias potential during umbrella sampling

[Viveca Lindahl]

Hi Meena,

No, they are not generally the same. The reaction coordinate using
'distance' is the norm of the COM distance vector (>=0). Using direction,
it's the projection onto the given vector (possibly negative).


--
Viveca


On Fri, May 11, 2018 at 11:33 AM, Meena Singh  wrote:

> Dear GROMACS users,
>
> Currently I am doing umbrella sampling for adsorption of molecule on solid
> surface. I have frozen the coordinates for solid surface and pulling the
> molecule towards the surface.
>
> I would like to know that while using options pull-geometry = distance and
> pull-dim = N N Y is same as the options pull-geometry = direction and
> pull-vec = 0 0 1?
>
> I am confused regarding the bias potential applied on the molecule, whether
> it is applied in all x, y, z coordinate of molecule or only in z coordinate
> of molecule for the above two scenarios?
>
> Thanking in advance for the help.
>
> Regards
>
> Meena Singh
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Re: [gmx-users] Non integer charge value

[Justin Lemkul]

On 5/11/18 6:20 AM, Hemalatha Jayabal wrote:

I apologize for the previous formatting.


Well it's no better here but it's immediately clear you're still doing 
something wrong:



[ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 202 HYP rtp HYP q +1.2 1 NH3 202 HYP N 1 -0.3 14.007 ; qtot -0.3
2 HC 202 HYP H1 2 0.33 1.008 ; qtot 0.03 3 HC 202 HYP H2 3 0.33 1.008 ;
qtot 0.36 4 HC 202 HYP H3 4 0.33 1.008 ; qtot 0.69 5 CT1 202 HYP CA 5 0.21


These charges are incorrect right off the bat. The [ PRO-NH2+ ] terminus 
has charges of -0.07 on N (with an atom type of NP), CA and CD are +0.16 
(types CP1 and CP3, respectively) and the two H atoms should have a 
charge of +0.24.


Without seeing what your full pdb2gmx command and screen output are, 
there's no way for any of us to know what you're doing incorrectly, but 
that's the source of the problem.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] KCl forms crystals at c=0.15M with amber99sb-ildn

[Justin Lemkul]

On 5/11/18 11:19 AM, Mark Abraham wrote:

Hi,

On Fri, May 11, 2018 at 12:07 PM Daniel Bauer 
wrote:


Hi,

thanks for the response! Now i know what I have to do :)

So did I understand you right that the ion parameters that are currently
used in amber99sb by GROMACS are not identical with the ones implemented
in the current version of amber99sb used by AMBER?


Please everybody be very careful with statements like this. Generally the
definition of a force field should never change, so that results remain
reproducible. This is why derivatives of forcefields have been made, while
correcting some observed deficiencies. However, since e.g. the original
validation of the AMBER ports within GROMACS were made against AMBER 8,
there have been some corrections of typos, etc. made by AMBER developers,
which AFAIK have all made their way to the GROMACS files.



If yes, whats the
reason for this (might be more of a question for Justin or Mark). Are
there any plans to change this in future releases?


First let's clarify whether anything really had its definition changed ;-)
If there's a recognized variant, then e.g. someone might contribute it to
http://www.gromacs.org/Downloads/User_contributions/Force_fields so that
people using it understand that it's a case of "buyer beware." These days
we feel it would not be appropriate to add support for a new force field in
GROMACS (say, CHARMM36) unless that change came alongside scripts that
would be able to verify that the implementation remains correct, even
though both GROMACS and the software for which it was developed will have
to change as time passes. (So that issues like
https://redmine.gromacs.org/issues/2046 are found and prevented early.)


I would also add on that it is common to see AMBER force fields used 
with a wide range of different ion parameters, based on what individual 
authors/groups find to be most effective. There are many, diverging 
variants of AMBER biomolecular force fields as well as ion parameters. 
AMBER99SB formally refers to a variant of the protein force field, and 
is coupled with standard ions. This is the "default" AMBER approach 
unless updated ion parameters are then employed in conjunction with the 
biomolecular force field. It becomes somewhat hard for the GROMACS 
implementation to satisfy the flexibility that other proteins like AMBER 
and CHARMM offer in terms of user-selected parameters that can be chosen 
on the fly.


Perhaps the only thing we can change on our end is documentation, e.g. 
in forcefield.doc or the manual that says "standard ion parameters are 
used" and it's up to the user to employ something else that is better 
should s/he choose.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] V2018.1 building issues

[Mark Abraham]

Hi,

I'm surprised that was able to work in 2016, but nevertheless it was never
designed to work and should not be relied upon. Build a separate binary for
each hardware flavor and have the module system choose the correct one to
load, per our installation guide
http://manual.gromacs.org/documentation/2018/install-guide/index.html#portability-aspects


Mark

On Thu, May 10, 2018 at 4:17 PM kevin chen  wrote:

> Hi  Gromacs Users,
>
> I'm having this weird issue while trying to build the new V2018.1 on
> Stampede2, which has both SKX amd KNL nodes on it. For V2016 and older, in
> order to run the same executable(mdrun_mpi), we have to build the "fat"
> binary with " -DGMX_SIMD=AVX_512" and "-DCMAKE_C_FLAGS="-O3 -xCORE-AVX2
> -axCORE-AVX512,MIC-AVX512 ". That actually worked just fine for V2016. We
> can actually run simulation on both skx and knl without any issues using
> the same binary. However, for some reason the same trick no longer works
> with V2018.1. We tried to build V2018.1 with the exactly same building
> script with " -DGMX_SIMD=AVX_512" option applied. This time around the
> binary(mdrun_mpi) only works on skx node but no on knls. So I was wondering
> is there any thing change since V2016 causing this issue or am I missing
> anything here? Thanks advanced for any pointers you guys might provide.
>
> Our building environment,
>
> Currently Loaded Modules:
>   1) intel/17.0.4   3) git/2.9.0   5) python/2.7.13   7) TACC
>   2) impi/17.0.34) autotools/1.1   6) xalt/1.7.7  8) cmake/3.10.2
>
> Best,
>
> Kevin
> --
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Re: [gmx-users] KCl forms crystals at c=0.15M with amber99sb-ildn

[Mark Abraham]

Hi,

On Fri, May 11, 2018 at 12:07 PM Daniel Bauer 
wrote:

> Hi,
>
> thanks for the response! Now i know what I have to do :)
>
> So did I understand you right that the ion parameters that are currently
> used in amber99sb by GROMACS are not identical with the ones implemented
> in the current version of amber99sb used by AMBER?


Please everybody be very careful with statements like this. Generally the
definition of a force field should never change, so that results remain
reproducible. This is why derivatives of forcefields have been made, while
correcting some observed deficiencies. However, since e.g. the original
validation of the AMBER ports within GROMACS were made against AMBER 8,
there have been some corrections of typos, etc. made by AMBER developers,
which AFAIK have all made their way to the GROMACS files.


> If yes, whats the
> reason for this (might be more of a question for Justin or Mark). Are
> there any plans to change this in future releases?
>

First let's clarify whether anything really had its definition changed ;-)
If there's a recognized variant, then e.g. someone might contribute it to
http://www.gromacs.org/Downloads/User_contributions/Force_fields so that
people using it understand that it's a case of "buyer beware." These days
we feel it would not be appropriate to add support for a new force field in
GROMACS (say, CHARMM36) unless that change came alongside scripts that
would be able to verify that the implementation remains correct, even
though both GROMACS and the software for which it was developed will have
to change as time passes. (So that issues like
https://redmine.gromacs.org/issues/2046 are found and prevented early.)

Mark

Best regards,
>
> Daniel
>
>
> On 05/08/2018 04:18 PM, Felipe Merino wrote:
> > Hi,
> >
> > I think the problem comes from the ion parameters within the "vanilla"
> > amber forcefieCld. If I'm not mistaken, the parameters in the gromacs
> > port are the Aqvist parameters, which are known to make this little
> > trick. In the past, we have used the Smith/Dang parameters for
> > simulations nucleic acids (Dang LX (1995)  J Am Chem Soc 117:
> > 6954–6960) although I think amber is using now Tom Cheatham's
> > parameters (J. Phys. Chem. B, 2008, 112 (30), pp 9020–9041).
> >
> > I hope that helps
> > Best
> > Felipe
> >
> > On 08/05/18 15:54, Daniel Bauer wrote:
> >> Hello,
> >>
> >>
> >> We are trying to use amber99sb-ildn with gromacs2018.1 for simulations
> >> of a protein in a salt solution. However, we observed that KCl seems to
> >> form stable salt crystals even at concentrations as low as 0.15 mol/l at
> >> T=298K in our system. Our MDP options have been taken from
> >> 10.5281/zenodo.1010238 and are listed below. It is reproducible with a
> >> system containing only 6000 TIP3P water molecules and 16 KCl (0.15M),
> >> generated by:
> >>
> >> gmx genconf -f spc216.gro -o waterbox.gro -nbox 3 3 3
> >>
> >> gmx grompp -f genions -c waterbox -o genions
> >>
> >> gmx genion -nname CL -pname K -conc 0.15 -s genions -p topol.top
> >>
> >>
> >> Does someone have an explanation what might cause this to happen? Our
> >> MDP options are listed below and an RDF showing the accumulation is
> >> attached.
> >>
> >>
> >> Best Regards,
> >>
> >> Daniel
> >>
> >>
> >> Command line:
> >> ;  gmx grompp -f md.mdp -c em/em -o md/md.tpr
> >>
> >> ; RUN CONTROL PARAMETERS
> >> integrator   = md
> >> tinit= 0
> >> dt   = 0.002
> >> nsteps   = 125
> >> init-step= 0
> >> simulation-part  = 1
> >> comm-mode= Linear
> >> nstcomm  = 1
> >> comm-grps= System
> >>
> >> ; NEIGHBORSEARCHING PARAMETERS
> >> cutoff-scheme= Verlet
> >> nstlist  = 10
> >> ns-type  = Grid
> >> pbc  = xyz
> >> periodic-molecules   = no
> >> verlet-buffer-tolerance  = 0.005
> >> rlist= 1.0
> >>
> >> ; OPTIONS FOR ELECTROSTATICS AND VDW
> >> ; Method for doing electrostatics
> >> coulombtype  = pme
> >> coulomb-modifier = Potential-shift-Verlet
> >> rcoulomb-switch  = 0
> >> rcoulomb = 1.0
> >> epsilon-r= 1
> >> epsilon-rf   = 0
> >> vdw-type = Cut-off
> >> vdw-modifier = Potential-shift-Verlet
> >> ; cut-off lengths
> >> rvdw-switch  = 0
> >> rvdw = 1.0
> >> DispCorr = EnerPres
> >> table-extension  = 1
> >> energygrp-table  =
> >> fourierspacing   = 0.12
> >> fourier-nx   = 0
> >> fourier-ny   = 0
> >> fourier-nz   = 0
> >> pme-order= 4
> >> ewald-rtol   = 1e-05
> >> ewald-rtol-lj= 0.001
> >> lj-pme-comb-rule = Geometric
> >> ewald-geometry   = 3d
> >> epsilon-surface  = 

Re: [gmx-users] KCl forms crystals at c=0.15M with amber99sb-ildn

[Daniel Bauer]

Hi,

thanks for the response! Now i know what I have to do :)

So did I understand you right that the ion parameters that are currently
used in amber99sb by GROMACS are not identical with the ones implemented
in the current version of amber99sb used by AMBER? If yes, whats the
reason for this (might be more of a question for Justin or Mark). Are
there any plans to change this in future releases?


Best regards,

Daniel


On 05/08/2018 04:18 PM, Felipe Merino wrote:
> Hi,
>
> I think the problem comes from the ion parameters within the "vanilla"
> amber forcefieCld. If I'm not mistaken, the parameters in the gromacs
> port are the Aqvist parameters, which are known to make this little
> trick. In the past, we have used the Smith/Dang parameters for
> simulations nucleic acids (Dang LX (1995)  J Am Chem Soc 117:
> 6954–6960) although I think amber is using now Tom Cheatham's
> parameters (J. Phys. Chem. B, 2008, 112 (30), pp 9020–9041).
>
> I hope that helps
> Best
> Felipe
>
> On 08/05/18 15:54, Daniel Bauer wrote:
>> Hello,
>>
>>
>> We are trying to use amber99sb-ildn with gromacs2018.1 for simulations
>> of a protein in a salt solution. However, we observed that KCl seems to
>> form stable salt crystals even at concentrations as low as 0.15 mol/l at
>> T=298K in our system. Our MDP options have been taken from
>> 10.5281/zenodo.1010238 and are listed below. It is reproducible with a
>> system containing only 6000 TIP3P water molecules and 16 KCl (0.15M),
>> generated by:
>>
>> gmx genconf -f spc216.gro -o waterbox.gro -nbox 3 3 3
>>
>> gmx grompp -f genions -c waterbox -o genions
>>
>> gmx genion -nname CL -pname K -conc 0.15 -s genions -p topol.top
>>
>>
>> Does someone have an explanation what might cause this to happen? Our
>> MDP options are listed below and an RDF showing the accumulation is
>> attached.
>>
>>
>> Best Regards,
>>
>> Daniel
>>
>>
>> Command line:
>> ;      gmx grompp -f md.mdp -c em/em -o md/md.tpr
>>
>> ; RUN CONTROL PARAMETERS
>> integrator   = md
>> tinit    = 0
>> dt   = 0.002
>> nsteps   = 125
>> init-step    = 0
>> simulation-part  = 1
>> comm-mode    = Linear
>> nstcomm  = 1
>> comm-grps    = System
>>
>> ; NEIGHBORSEARCHING PARAMETERS
>> cutoff-scheme    = Verlet
>> nstlist  = 10
>> ns-type  = Grid
>> pbc  = xyz
>> periodic-molecules   = no
>> verlet-buffer-tolerance  = 0.005
>> rlist    = 1.0
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>> ; Method for doing electrostatics
>> coulombtype  = pme
>> coulomb-modifier = Potential-shift-Verlet
>> rcoulomb-switch  = 0
>> rcoulomb = 1.0
>> epsilon-r    = 1
>> epsilon-rf   = 0
>> vdw-type = Cut-off
>> vdw-modifier = Potential-shift-Verlet
>> ; cut-off lengths
>> rvdw-switch  = 0
>> rvdw = 1.0
>> DispCorr = EnerPres
>> table-extension  = 1
>> energygrp-table  =
>> fourierspacing   = 0.12
>> fourier-nx   = 0
>> fourier-ny   = 0
>> fourier-nz   = 0
>> pme-order    = 4
>> ewald-rtol   = 1e-05
>> ewald-rtol-lj    = 0.001
>> lj-pme-comb-rule = Geometric
>> ewald-geometry   = 3d
>> epsilon-surface  = 0
>>
>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
>> ; Temperature coupling
>> tcoupl   = V-rescale
>> nsttcouple   = -1
>> nh-chain-length  = 10
>> tc-grps  = System
>> tau_t    = 0.1
>> ref-t    = 298.0
>>
>> ; pressure coupling
>> Pcoupl   = Berendsen
>> Pcoupltype   = isotropic
>> nstpcouple   = -1
>> tau_p    = 4.0
>> compressibility  = 4.5e-5
>> ref_p    = 1.0
>> refcoord_scaling = all
>>
>> ; GENERATE VELOCITIES FOR STARTUP RUN
>> gen_vel  = yes
>> gen_temp = 298.0
>> gen_seed = -1
>>
>> ; OPTIONS FOR BONDS
>> constraints  = all-bonds
>> constraint_algorithm = lincs
>> continuation = no
>> lincs_order  = 4
>> lincs_iter   = 1
>> lincs-warnangle  = 30
>> morse    = no
>>
>>
>>
>>
>> Best Regards,
>>
>> Daniel
>>
>

-- 
Daniel Bauer, M.Sc.

TU Darmstadt
Computational Biology & Simulation
Schnittspahnstr. 2
64287 Darmstadt
ba...@cbs.tu-darmstadt.de

Don't trust atoms, they make up everything.

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Re: [gmx-users] Restarting crashed simmulation.

[neelam wafa]

Thanks Sir Justin!
I have continued the simmulation from the last step.

Regards

On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul  wrote:

>
>
> On 5/10/18 7:08 AM, neelam wafa wrote:
>
>> Hi gmx users!
>>
>> I am running a 5ns md simmulation of a protein with 250 steps. It
>> crashed at  136 steps due to some power problem. Now I want to
>> continue
>> this simmulation. In the manual following command is given:
>>
>> mdrun -s topol.tpr -cpi state.cpt
>>
>> but I am confused which file is state.cpt. I have got two cpt files
>> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?
>>
>
> Look at the time stamps of the files and inspect their contents with gmx
> check. You will see an obvious difference in what they contain. Also
> consult the mdrun help info, which specifically addresses your question.
>
> Also I did not get a md_1_0.gro file/ Is is due to incomplete simmulation?
>>
>
> Yes, because that file is only produced from the last step.
>
> Also do I need to specify  -append flag or not? I am using version 5.1.5
>>
>
> -append has been the default option for many years. Again, see the mdrun
> help description.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
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Re: [gmx-users] Non integer charge value

[Hemalatha Jayabal]

I apologize for the previous formatting.

[ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 202 HYP rtp HYP q +1.2 1 NH3 202 HYP N 1 -0.3 14.007 ; qtot -0.3
2 HC 202 HYP H1 2 0.33 1.008 ; qtot 0.03 3 HC 202 HYP H2 3 0.33 1.008 ;
qtot 0.36 4 HC 202 HYP H3 4 0.33 1.008 ; qtot 0.69 5 CT1 202 HYP CA 5 0.21
12.011 ; qtot 0.9 6 HB 202 HYP HA 6 0.1 1.008 ; qtot 1 7 C 202 HYP C 7 0.51
12.011 ; qtot 1.51 8 O 202 HYP O 8 -0.51 15.999 ; qtot 1 9 CP2 202 HYP CB 9
-0.18 12.011 ; qtot 0.82 10 HA 202 HYP HB1 10 0.09 1.008 ; qtot 0.91 11 HA
202 HYP HB2 11 0.09 1.008 ; qtot 1 12 CP2 202 HYP CG 12 0.14 12.011 ; qtot
1.14 13 HA 202 HYP HG 13 0.09 1.008 ; qtot 1.23 14 CP3 202 HYP CD 14 0
12.011 ; qtot 1.23 15 HA 202 HYP HD21 15 0.09 1.008 ; qtot 1.32 16 HA 202
HYP HD22 16 0.09 1.008 ; qtot 1.41 17 OH1 202 HYP OD1 17 -0.66 15.999 ;
qtot 0.75 18 H 202 HYP HD1 18 0.43 1.008 ; qtot 1.18 Sequence (From PDB
file) SEQRES 1 A 7 GLY PRO HYP GLY PRO HYP GLY SEQRES 1 B 7 HYP GLY PRO HYP
GLY PRO HYP SEQRES 1 C 7 PRO HYP GLY PRO HYP GLY PRO The below is the
topology where the residue is not present as termini ; residue 205 HYP rtp
HYP q 0.0 40 N 205 HYP N 40 -0.29 14.007 ; qtot 0.89 41 CP1 205 HYP CA 41
0.02 12.011 ; qtot 0.91 42 HB 205 HYP HA 42 0.09 1.008 ; qtot 1 43 C 205
HYP C 43 0.51 12.011 ; qtot 1.51 44 O 205 HYP O 44 -0.51 15.999 ; qtot 1 45
CP2 205 HYP CB 45 -0.18 12.011 ; qtot 0.82 46 HA 205 HYP HB1 46 0.09 1.008
; qtot 0.91 47 HA 205 HYP HB2 47 0.09 1.008 ; qtot 1 48 CP2 205 HYP CG 48
0.14 12.011 ; qtot 1.14 49 HA 205 HYP HG 49 0.09 1.008 ; qtot 1.23 50 CP3
205 HYP CD 50 0 12.011 ; qtot 1.23 51 HA 205 HYP HD21 51 0.09 1.008 ; qtot
1.32 52 HA 205 HYP HD22 52 0.09 1.008 ; qtot 1.41 53 OH1 205 HYP OD1 53
-0.66 15.999 ; qtot 0.75 54 H 205 HYP HD1 54 0.43 1.008 ; qtot 1.18

On 11-May-2018 12:06, "Hemalatha Jayabal" 
wrote:

I applied the said terminus as well but I ended up getting the same error.


[ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 202 HYP rtp HYP q +1.2 1 NH3 202 HYP N 1 -0.3 14.007 ; qtot -0.3
2 HC 202 HYP H1 2 0.33 1.008 ; qtot 0.03 3 HC 202 HYP H2 3 0.33 1.008 ;
qtot 0.36 4 HC 202 HYP H3 4 0.33 1.008 ; qtot 0.69 5 CT1 202 HYP CA 5 0.21
12.011 ; qtot 0.9 6 HB 202 HYP HA 6 0.1 1.008 ; qtot 1 7 C 202 HYP C 7 0.51
12.011 ; qtot 1.51 8 O 202 HYP O 8 -0.51 15.999 ; qtot 1 9 CP2 202 HYP CB 9
-0.18 12.011 ; qtot 0.82 10 HA 202 HYP HB1 10 0.09 1.008 ; qtot 0.91 11 HA
202 HYP HB2 11 0.09 1.008 ; qtot 1 12 CP2 202 HYP CG 12 0.14 12.011 ; qtot
1.14 13 HA 202 HYP HG 13 0.09 1.008 ; qtot 1.23 14 CP3 202 HYP CD 14 0
12.011 ; qtot 1.23 15 HA 202 HYP HD21 15 0.09 1.008 ; qtot 1.32 16 HA 202
HYP HD22 16 0.09 1.008 ; qtot 1.41 17 OH1 202 HYP OD1 17 -0.66 15.999 ;
qtot 0.75 18 H 202 HYP HD1 18 0.43 1.008 ; qtot 1.18 Sequence (From PDB
file) SEQRES 1 A 7 GLY PRO HYP GLY PRO HYP GLY SEQRES 1 B 7 HYP GLY PRO HYP
GLY PRO HYP SEQRES 1 C 7 PRO HYP GLY PRO HYP GLY PRO The below is the
topology where the residue is not present as termini ; residue 205 HYP rtp
HYP q 0.0 40 N 205 HYP N 40 -0.29 14.007 ; qtot 0.89 41 CP1 205 HYP CA 41
0.02 12.011 ; qtot 0.91 42 HB 205 HYP HA 42 0.09 1.008 ; qtot 1 43 C 205
HYP C 43 0.51 12.011 ; qtot 1.51 44 O 205 HYP O 44 -0.51 15.999 ; qtot 1 45
CP2 205 HYP CB 45 -0.18 12.011 ; qtot 0.82 46 HA 205 HYP HB1 46 0.09 1.008
; qtot 0.91 47 HA 205 HYP HB2 47 0.09 1.008 ; qtot 1 48 CP2 205 HYP CG 48
0.14 12.011 ; qtot 1.14 49 HA 205 HYP HG 49 0.09 1.008 ; qtot 1.23 50 CP3
205 HYP CD 50 0 12.011 ; qtot 1.23 51 HA 205 HYP HD21 51 0.09 1.008 ; qtot
1.32 52 HA 205 HYP HD22 52 0.09 1.008 ; qtot 1.41 53 OH1 205 HYP OD1 53
-0.66 15.999 ; qtot 0.75 54 H 205 HYP HD1 54 0.43 1.008 ; qtot 1.18


  Thank you!



On Fri 11 May, 2018, 00:11 Justin Lemkul,  wrote:

>
>
> On 5/10/18 8:57 AM, Hemalatha Jayabal wrote:
> > The magnitude of the charge is 0.18 and I hope such magnitude cannot be
> > ignored. Please find the topology of the protein chain(specific residue)
> in
> > which the error is occuring
> > [ atoms ]
> > ;   nr   type  resnr residue  atom   cgnr charge   mass
> typeB
> >chargeB  massB
> > ; residue 202 HYP rtp HYP  q +0.2
> >   1NH2202HYP  N  1  -0.96 14.007   ;
> > qtot -0.96
> >   2  H202HYPHT1  2   0.34  1.008   ;
> > qtot -0.62
> >   3  H202HYPHT2  3   0.34  1.008   ;
> > qtot -0.28
>
> What patching are you applying to the N-terminus? These charges are
> totally wrong. Make sure to apply the PRO-NH2+ patch.
>
> -Justin
>
> >   4CT1202HYP CA  4   0.19 12.011   ;
> > qtot -0.09
> >   5 HB202HYP HA  5   0.09  1.008   ;
> > qtot 0
> >   6  C202HYP  C  6   0.51 12.011   ;
> > qtot 0.51
> >   7  O202HYP  O  7  -0.51 15.999   ;
> > 

[gmx-users] Bias potential during umbrella sampling

[Meena Singh]

Dear GROMACS users,

Currently I am doing umbrella sampling for adsorption of molecule on solid
surface. I have frozen the coordinates for solid surface and pulling the
molecule towards the surface.

I would like to know that while using options pull-geometry = distance and
pull-dim = N N Y is same as the options pull-geometry = direction and
pull-vec = 0 0 1?

I am confused regarding the bias potential applied on the molecule, whether
it is applied in all x, y, z coordinate of molecule or only in z coordinate
of molecule for the above two scenarios?

Thanking in advance for the help.

Regards

Meena Singh
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Re: [gmx-users] Non integer charge value

[Hemalatha Jayabal]

I applied the said terminus as well but I ended up getting the same error.


[ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 202 HYP rtp HYP q +1.2 1 NH3 202 HYP N 1 -0.3 14.007 ; qtot -0.3
2 HC 202 HYP H1 2 0.33 1.008 ; qtot 0.03 3 HC 202 HYP H2 3 0.33 1.008 ;
qtot 0.36 4 HC 202 HYP H3 4 0.33 1.008 ; qtot 0.69 5 CT1 202 HYP CA 5 0.21
12.011 ; qtot 0.9 6 HB 202 HYP HA 6 0.1 1.008 ; qtot 1 7 C 202 HYP C 7 0.51
12.011 ; qtot 1.51 8 O 202 HYP O 8 -0.51 15.999 ; qtot 1 9 CP2 202 HYP CB 9
-0.18 12.011 ; qtot 0.82 10 HA 202 HYP HB1 10 0.09 1.008 ; qtot 0.91 11 HA
202 HYP HB2 11 0.09 1.008 ; qtot 1 12 CP2 202 HYP CG 12 0.14 12.011 ; qtot
1.14 13 HA 202 HYP HG 13 0.09 1.008 ; qtot 1.23 14 CP3 202 HYP CD 14 0
12.011 ; qtot 1.23 15 HA 202 HYP HD21 15 0.09 1.008 ; qtot 1.32 16 HA 202
HYP HD22 16 0.09 1.008 ; qtot 1.41 17 OH1 202 HYP OD1 17 -0.66 15.999 ;
qtot 0.75 18 H 202 HYP HD1 18 0.43 1.008 ; qtot 1.18 Sequence (From PDB
file) SEQRES 1 A 7 GLY PRO HYP GLY PRO HYP GLY SEQRES 1 B 7 HYP GLY PRO HYP
GLY PRO HYP SEQRES 1 C 7 PRO HYP GLY PRO HYP GLY PRO The below is the
topology where the residue is not present as termini ; residue 205 HYP rtp
HYP q 0.0 40 N 205 HYP N 40 -0.29 14.007 ; qtot 0.89 41 CP1 205 HYP CA 41
0.02 12.011 ; qtot 0.91 42 HB 205 HYP HA 42 0.09 1.008 ; qtot 1 43 C 205
HYP C 43 0.51 12.011 ; qtot 1.51 44 O 205 HYP O 44 -0.51 15.999 ; qtot 1 45
CP2 205 HYP CB 45 -0.18 12.011 ; qtot 0.82 46 HA 205 HYP HB1 46 0.09 1.008
; qtot 0.91 47 HA 205 HYP HB2 47 0.09 1.008 ; qtot 1 48 CP2 205 HYP CG 48
0.14 12.011 ; qtot 1.14 49 HA 205 HYP HG 49 0.09 1.008 ; qtot 1.23 50 CP3
205 HYP CD 50 0 12.011 ; qtot 1.23 51 HA 205 HYP HD21 51 0.09 1.008 ; qtot
1.32 52 HA 205 HYP HD22 52 0.09 1.008 ; qtot 1.41 53 OH1 205 HYP OD1 53
-0.66 15.999 ; qtot 0.75 54 H 205 HYP HD1 54 0.43 1.008 ; qtot 1.18


  Thank you!



On Fri 11 May, 2018, 00:11 Justin Lemkul,  wrote:

>
>
> On 5/10/18 8:57 AM, Hemalatha Jayabal wrote:
> > The magnitude of the charge is 0.18 and I hope such magnitude cannot be
> > ignored. Please find the topology of the protein chain(specific residue)
> in
> > which the error is occuring
> > [ atoms ]
> > ;   nr   type  resnr residue  atom   cgnr charge   mass
> typeB
> >chargeB  massB
> > ; residue 202 HYP rtp HYP  q +0.2
> >   1NH2202HYP  N  1  -0.96 14.007   ;
> > qtot -0.96
> >   2  H202HYPHT1  2   0.34  1.008   ;
> > qtot -0.62
> >   3  H202HYPHT2  3   0.34  1.008   ;
> > qtot -0.28
>
> What patching are you applying to the N-terminus? These charges are
> totally wrong. Make sure to apply the PRO-NH2+ patch.
>
> -Justin
>
> >   4CT1202HYP CA  4   0.19 12.011   ;
> > qtot -0.09
> >   5 HB202HYP HA  5   0.09  1.008   ;
> > qtot 0
> >   6  C202HYP  C  6   0.51 12.011   ;
> > qtot 0.51
> >   7  O202HYP  O  7  -0.51 15.999   ;
> > qtot 0
> >   8CP2202HYP CB  8  -0.18 12.011   ;
> > qtot -0.18
> >   9 HA202HYPHB1  9   0.09  1.008   ;
> > qtot -0.09
> >  10 HA202HYPHB2 10   0.09  1.008   ;
> > qtot 0
> >  11CP2202HYP CG 11   0.14 12.011   ;
> > qtot 0.14
> >  12 HA202HYP HG 12   0.09  1.008   ;
> > qtot 0.23
> >  13CP3202HYP CD 13  0 12.011   ;
> > qtot 0.23
> >  14 HA202HYP   HD21 14   0.09  1.008   ;
> > qtot 0.32
> >  15 HA202HYP   HD22 15   0.09  1.008   ;
> > qtot 0.41
> >  16OH1202HYPOD1 16  -0.66 15.999   ;
> > qtot -0.25
> >  17  H202HYPHD1 17   0.43  1.008   ;
> > qtot 0.18
> >
> >
> >
> > On Thu 10 May, 2018, 18:07 Justin Lemkul,  wrote:
> >
> >>
> >> On 5/10/18 8:29 AM, Hemalatha Jayabal wrote:
> >>> Hi all,
> >>>
> >>> I have added a non standard amino acid 'Hydroxyproline' to my
> forcefield
> >>> (from literature) Charmm27 and after using pdb2gmx i could see that the
> >>> system has a non integer charge value for 1 protein chain out of 3
> >> protein
> >>> chains.  (All 3 chains contain the non standard amino acid)
> >>>The problem is occuring in the chain in which the terminal residue
> is
> >> this
> >>> hydroxyproline. (All other places where the 'HYP' residue appears, the
> >>> charge is 0). I tried using different terminii just to be sure that the
> >>> problem is not because of the terminii.
> >>>
> >>> What should be done in such a case?
> >> That depends on if the magnitude of the charge is meaningful or not. If
> >> you have two "correct" chains and one "incorrect" chain, that suggests
> >> that