Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.

[rajat desikan]

Thank you!


On Mon, Jul 15, 2013 at 6:29 PM, Justin Lemkul  wrote:

>
>
> On 7/15/13 8:56 AM, rajat desikan wrote:
>
>> I guess, the more important question is whether the checkpoint file stores
>> the previous checkpoints as well. If it stores only the last checkpoint at
>> 20 ns, then I guess there is no way to rerun from 18 ns.
>>
>>
> It does not.  Checkpoints are recycled every -cpt minutes.  You can keep
> all checkpoints by using the mdrun -cpnum option, but I suspect that will
> use up a lot of disk space.
>
>
>  I do not store a .trr because of space constraints and hence I do not have
>> the velocities. otherwise, I would have used the snapshot from 18ns and
>> extended the simulation. Now, it looks like I will have to re-generate the
>> velocities and re-equilibrate the system.
>>
>>
> Or just re-run the simulation from the same .tpr file you used before.
>
> -Justin
>
>
>> On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan > >wrote:
>>
>>  Hi Justin,
>>> The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation
>>> will finish in one step.
>>>
>>>
>>> On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul  wrote:
>>>
>>>

 On 7/15/13 8:38 AM, Rajat Desikan wrote:

  Hi,
> I have a 20 ns long trajectory which has become corrupted beyond 18ns.
> I
> have the full checkpoint file. Is there any way I can use mdrun and the
> .cpt
> to rerun the simulation from 18ns and append it to the current .xtc
> (After I
> have clipped the part beyond 18ns by trjconv)? I did not find the
> appropriate flag in the mdrun online manual pages.
>
>
 It's no different than doing any restart.

 mdrun -s topol.tpr -cpi good_state.cpt -noappend

 Then concatenate trajectory and energy files with trjcat and eneconv.

 -Justin

 --
 ==


 Justin A. Lemkul, Ph.D.
 Postdoctoral Associate

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalemkul@outerbanks.umaryland.edu >>> umaryland.edu >| (410) 706-7441

 ==

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>>>
>>>
>>> --
>>> Rajat Desikan (Ph.D Scholar)
>>> Prof. K. Ganapathy Ayappa's Lab (no 13),
>>> Dept. of Chemical Engineering,
>>> Indian Institute of Science, Bangalore
>>>
>>>
>>
>>
>>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Associate
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  |
> (410) 706-7441
>
> ==**
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>



-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.

[Justin Lemkul]

On 7/15/13 8:56 AM, rajat desikan wrote:

I guess, the more important question is whether the checkpoint file stores
the previous checkpoints as well. If it stores only the last checkpoint at
20 ns, then I guess there is no way to rerun from 18 ns.



It does not.  Checkpoints are recycled every -cpt minutes.  You can keep all 
checkpoints by using the mdrun -cpnum option, but I suspect that will use up a 
lot of disk space.



I do not store a .trr because of space constraints and hence I do not have
the velocities. otherwise, I would have used the snapshot from 18ns and
extended the simulation. Now, it looks like I will have to re-generate the
velocities and re-equilibrate the system.



Or just re-run the simulation from the same .tpr file you used before.

-Justin



On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan wrote:


Hi Justin,
The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation
will finish in one step.


On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul  wrote:




On 7/15/13 8:38 AM, Rajat Desikan wrote:


Hi,
I have a 20 ns long trajectory which has become corrupted beyond 18ns. I
have the full checkpoint file. Is there any way I can use mdrun and the
.cpt
to rerun the simulation from 18ns and append it to the current .xtc
(After I
have clipped the part beyond 18ns by trjconv)? I did not find the
appropriate flag in the mdrun online manual pages.



It's no different than doing any restart.

mdrun -s topol.tpr -cpi good_state.cpt -noappend

Then concatenate trajectory and energy files with trjcat and eneconv.

-Justin

--
==**

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul@outerbanks.umaryland.**edu | (410) 
706-7441

==**

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--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore







--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.

[Justin Lemkul]

On 7/15/13 8:52 AM, rajat desikan wrote:

Hi Justin,
The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation
will finish in one step.



You need a checkpoint file that corresponds to a good frame before the 
corruption.  If you don't have that, you can't fix the broken trajectory.  Your 
first message implied that you had a good frame.  Since that's not the case, 
you'll have to either re-run the simulation or skip the bad frame and settle for 
fewer data points.


-Justin



On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul  wrote:




On 7/15/13 8:38 AM, Rajat Desikan wrote:


Hi,
I have a 20 ns long trajectory which has become corrupted beyond 18ns. I
have the full checkpoint file. Is there any way I can use mdrun and the
.cpt
to rerun the simulation from 18ns and append it to the current .xtc
(After I
have clipped the part beyond 18ns by trjconv)? I did not find the
appropriate flag in the mdrun online manual pages.



It's no different than doing any restart.

mdrun -s topol.tpr -cpi good_state.cpt -noappend

Then concatenate trajectory and energy files with trjcat and eneconv.

-Justin

--
==**

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul@outerbanks.umaryland.**edu  |
(410) 706-7441

==**

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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
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Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.

[rajat desikan]

I guess, the more important question is whether the checkpoint file stores
the previous checkpoints as well. If it stores only the last checkpoint at
20 ns, then I guess there is no way to rerun from 18 ns.

I do not store a .trr because of space constraints and hence I do not have
the velocities. otherwise, I would have used the snapshot from 18ns and
extended the simulation. Now, it looks like I will have to re-generate the
velocities and re-equilibrate the system.


On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan wrote:

> Hi Justin,
> The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation
> will finish in one step.
>
>
> On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 7/15/13 8:38 AM, Rajat Desikan wrote:
>>
>>> Hi,
>>> I have a 20 ns long trajectory which has become corrupted beyond 18ns. I
>>> have the full checkpoint file. Is there any way I can use mdrun and the
>>> .cpt
>>> to rerun the simulation from 18ns and append it to the current .xtc
>>> (After I
>>> have clipped the part beyond 18ns by trjconv)? I did not find the
>>> appropriate flag in the mdrun online manual pages.
>>>
>>
>> It's no different than doing any restart.
>>
>> mdrun -s topol.tpr -cpi good_state.cpt -noappend
>>
>> Then concatenate trajectory and energy files with trjcat and eneconv.
>>
>> -Justin
>>
>> --
>> ==**
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Associate
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul@outerbanks.umaryland.**edu | 
>> (410) 706-7441
>>
>> ==**
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>
>
>
> --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
>



-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
-- 
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Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.

[rajat desikan]

Hi Justin,
The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation
will finish in one step.


On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul  wrote:

>
>
> On 7/15/13 8:38 AM, Rajat Desikan wrote:
>
>> Hi,
>> I have a 20 ns long trajectory which has become corrupted beyond 18ns. I
>> have the full checkpoint file. Is there any way I can use mdrun and the
>> .cpt
>> to rerun the simulation from 18ns and append it to the current .xtc
>> (After I
>> have clipped the part beyond 18ns by trjconv)? I did not find the
>> appropriate flag in the mdrun online manual pages.
>>
>
> It's no different than doing any restart.
>
> mdrun -s topol.tpr -cpi good_state.cpt -noappend
>
> Then concatenate trajectory and energy files with trjcat and eneconv.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Associate
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  |
> (410) 706-7441
>
> ==**
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
-- 
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Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.

[Justin Lemkul]

On 7/15/13 8:38 AM, Rajat Desikan wrote:

Hi,
I have a 20 ns long trajectory which has become corrupted beyond 18ns. I
have the full checkpoint file. Is there any way I can use mdrun and the .cpt
to rerun the simulation from 18ns and append it to the current .xtc (After I
have clipped the part beyond 18ns by trjconv)? I did not find the
appropriate flag in the mdrun online manual pages.


It's no different than doing any restart.

mdrun -s topol.tpr -cpi good_state.cpt -noappend

Then concatenate trajectory and energy files with trjcat and eneconv.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
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[gmx-users] Using the checkpoint file to restore corrupt trajectory.

[Rajat Desikan]

Hi, 
I have a 20 ns long trajectory which has become corrupted beyond 18ns. I
have the full checkpoint file. Is there any way I can use mdrun and the .cpt
to rerun the simulation from 18ns and append it to the current .xtc (After I
have clipped the part beyond 18ns by trjconv)? I did not find the
appropriate flag in the mdrun online manual pages. 
Thanks.



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