date:20130917

when i use following  omment for restart

mdrun -s md.tpr -cpi md.cpt
i get following error

Output file appending has been requested,
but some output files listed in the checkpoint file md.cpt
are not present or are named differently by the current program:
output files present: md.log
output files not present or named differently: md.trr md.edr
  

but i have md.trr  and md.edr in my folder.

thank you so much


- Forwarded Message -
From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Tuesday, September 17, 2013 11:22 AM
Subject: Re: [gmx-users] How to restart the crashed run
 

Hi,

Please keep discussion on the mailing list.

If you have a .cpt file that is not called state.cpt, then you must
have asked for the checkpoint file to be named md.cpt in your original
mdrun command (e.g. with mdrun -cpo md). state.cpt is simply the
default filename (and mostly there is no reason to change that).
Simply use md.cpt, now that you have it :-)

Mark


On Tue, Sep 17, 2013 at 2:49 AM, Mahboobeh Eslami
 wrote:
> I have md.cpt but I don't have restart my run
> What is the purpose of the state.cpt file?
> thank you so much
>
> From: Mark Abraham 
> To: Mahboobeh Eslami ; Discussion list for
> GROMACS users 
> Sent: Tuesday, September 17, 2013 9:36 AM
> Subject: Re: [gmx-users] How to restart the crashed run
>
> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests
> the 3.x-era restart strategy when checkpoint files are unavailable.
> But if you simply have no output files, then you have no ability to
> restart.
>
> Mark
>
> On Tue, Sep 17, 2013 at 1:59 AM, Mahboobeh Eslami
>  wrote:
>> hi my friends
>>
>> please help me
>>
>> i did 20 ns simulation by gromacs 4.5.5 but the power was shut down near
>> the end of the simulation
>> How to restart the crashed run?
>>
>>  in the gromacs.org following comment has been proposed
>>
>> mdrun -s topol.tpr -cpi state.cpt
>>
>> but i don't have state.cpt in my folder.
>>
>> I need urgent help
>> Thank you very much
>>
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
-- 
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] How to restart the crashed run

You named them last time you ran mdrun, either explicitly or with
-deffnm. Do the same.

Mark

On Tue, Sep 17, 2013 at 3:19 AM, Mahboobeh Eslami
 wrote:
> when i use following  omment for restart
>
> mdrun -s md.tpr -cpi md.cpt
> i get following error
>
> Output file appending has been requested,
> but some output files listed in the checkpoint file md.cpt
> are not present or are named differently by the current program:
> output files present: md.log
> output files not present or named differently: md.trr md.edr
>
>
> but i have md.trr  and md.edr in my folder.
>
> thank you so much
>
>
> - Forwarded Message -
> From: Mark Abraham 
> To: Discussion list for GROMACS users 
> Sent: Tuesday, September 17, 2013 11:22 AM
> Subject: Re: [gmx-users] How to restart the crashed run
>
>
> Hi,
>
> Please keep discussion on the mailing list.
>
> If you have a .cpt file that is not called state.cpt, then you must
> have asked for the checkpoint file to be named md.cpt in your original
> mdrun command (e.g. with mdrun -cpo md). state.cpt is simply the
> default filename (and mostly there is no reason to change that).
> Simply use md.cpt, now that you have it :-)
>
> Mark
>
>
> On Tue, Sep 17, 2013 at 2:49 AM, Mahboobeh Eslami
>  wrote:
>> I have md.cpt but I don't have restart my run
>> What is the purpose of the state.cpt file?
>> thank you so much
>>
>> From: Mark Abraham 
>> To: Mahboobeh Eslami ; Discussion list for
>> GROMACS users 
>> Sent: Tuesday, September 17, 2013 9:36 AM
>> Subject: Re: [gmx-users] How to restart the crashed run
>>
>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests
>> the 3.x-era restart strategy when checkpoint files are unavailable.
>> But if you simply have no output files, then you have no ability to
>> restart.
>>
>> Mark
>>
>> On Tue, Sep 17, 2013 at 1:59 AM, Mahboobeh Eslami
>>  wrote:
>>> hi my friends
>>>
>>> please help me
>>>
>>> i did 20 ns simulation by gromacs 4.5.5 but the power was shut down near
>>> the end of the simulation
>>> How to restart the crashed run?
>>>
>>>  in the gromacs.org following comment has been proposed
>>>
>>> mdrun -s topol.tpr -cpi state.cpt
>>>
>>> but i don't have state.cpt in my folder.
>>>
>>> I need urgent help
>>> Thank you very much
>>>
>>> --
>>> 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/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
> --
> 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/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> 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/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Fw: [gmx-users] How to restart the crashed run

dear mark

yes i do
my comment for md run was following


mdrun -v -deffnm md >& md.job &

now what comment is true for restart? 
I've recently started working with the gromacs and i am not professional
 thank you and best wishes for you

- Forwarded Message -
From: Mark Abraham 
To: Mahboobeh Eslami ; Discussion list for GROMACS 
users  
Sent: Tuesday, September 17, 2013 12:23 PM
Subject: Re: [gmx-users] How to restart the crashed run
 

You named them last time you ran mdrun, either explicitly or with
-deffnm. Do the same.

Mark

On Tue, Sep 17, 2013 at 3:19 AM, Mahboobeh Eslami
 wrote:
> when i use following  omment for restart
>
> mdrun -s md.tpr -cpi md.cpt
> i get following error
>
> Output file appending has been requested,
> but some output files listed in the checkpoint file md.cpt
> are not present or are named differently by the current program:
> output files present: md.log
> output files not present or named differently: md.trr md.edr
>
>
> but i have md.trr  and md.edr in my folder.
>
> thank you so much
>
>
> - Forwarded Message -
> From: Mark Abraham 
> To: Discussion list for GROMACS users 
> Sent: Tuesday, September 17, 2013 11:22 AM
> Subject: Re: [gmx-users] How to restart the crashed run
>
>
> Hi,
>
> Please keep discussion on the mailing list.
>
> If you have a .cpt file that is not called state.cpt, then you must
> have asked for the checkpoint file to be named md.cpt in your original
> mdrun command (e.g. with mdrun -cpo md). state.cpt is simply the
> default filename (and mostly there is no reason to change that).
> Simply use md.cpt, now that you have it :-)
>
> Mark
>
>
> On Tue, Sep 17, 2013 at 2:49 AM, Mahboobeh Eslami
>  wrote:
>> I have md.cpt but I don't have restart my run
>> What is the purpose of the state.cpt file?
>> thank you so much
>>
>> From: Mark Abraham 
>> To: Mahboobeh Eslami ; Discussion list for
>> GROMACS users 
>> Sent: Tuesday, September 17, 2013 9:36 AM
>> Subject: Re: [gmx-users] How to restart the crashed run
>>
>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests
>> the 3.x-era restart strategy when checkpoint files are unavailable.
>> But if you simply have no output files, then you have no ability to
>> restart.
>>
>> Mark
>>
>> On Tue, Sep 17, 2013 at 1:59 AM, Mahboobeh Eslami
>>  wrote:
>>> hi my friends
>>>
>>> please help me
>>>
>>> i did 20 ns simulation by gromacs 4.5.5 but the power was shut down near
>>> the end of the simulation
>>> How to restart the crashed run?
>>>
>>>  in the gromacs.org following comment has been proposed
>>>
>>> mdrun -s topol.tpr -cpi state.cpt
>>>
>>> but i don't have state.cpt in my folder.
>>>
>>> I need urgent help
>>> Thank you very much
>>>
>>> --
>>> gmx-users mailing list    gmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: Fw: [gmx-users] How to restart the crashed run

mdrun -v -deffnm md -cpi md

IIRC the -cpi file is immune from -deffnm

Mark

On Tue, Sep 17, 2013 at 4:48 AM, Mahboobeh Eslami
 wrote:
> dear mark
>
> yes i do
> my comment for md run was following
>
>
> mdrun -v -deffnm md >& md.job &
>
> now what comment is true for restart?
> I've recently started working with the gromacs and i am not professional
>  thank you and best wishes for you
>
> - Forwarded Message -
> From: Mark Abraham 
> To: Mahboobeh Eslami ; Discussion list for 
> GROMACS users 
> Sent: Tuesday, September 17, 2013 12:23 PM
> Subject: Re: [gmx-users] How to restart the crashed run
>
>
> You named them last time you ran mdrun, either explicitly or with
> -deffnm. Do the same.
>
> Mark
>
> On Tue, Sep 17, 2013 at 3:19 AM, Mahboobeh Eslami
>  wrote:
>> when i use following  omment for restart
>>
>> mdrun -s md.tpr -cpi md.cpt
>> i get following error
>>
>> Output file appending has been requested,
>> but some output files listed in the checkpoint file md.cpt
>> are not present or are named differently by the current program:
>> output files present: md.log
>> output files not present or named differently: md.trr md.edr
>>
>>
>> but i have md.trr  and md.edr in my folder.
>>
>> thank you so much
>>
>>
>> - Forwarded Message -
>> From: Mark Abraham 
>> To: Discussion list for GROMACS users 
>> Sent: Tuesday, September 17, 2013 11:22 AM
>> Subject: Re: [gmx-users] How to restart the crashed run
>>
>>
>> Hi,
>>
>> Please keep discussion on the mailing list.
>>
>> If you have a .cpt file that is not called state.cpt, then you must
>> have asked for the checkpoint file to be named md.cpt in your original
>> mdrun command (e.g. with mdrun -cpo md). state.cpt is simply the
>> default filename (and mostly there is no reason to change that).
>> Simply use md.cpt, now that you have it :-)
>>
>> Mark
>>
>>
>> On Tue, Sep 17, 2013 at 2:49 AM, Mahboobeh Eslami
>>  wrote:
>>> I have md.cpt but I don't have restart my run
>>> What is the purpose of the state.cpt file?
>>> thank you so much
>>>
>>> From: Mark Abraham 
>>> To: Mahboobeh Eslami ; Discussion list for
>>> GROMACS users 
>>> Sent: Tuesday, September 17, 2013 9:36 AM
>>> Subject: Re: [gmx-users] How to restart the crashed run
>>>
>>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests
>>> the 3.x-era restart strategy when checkpoint files are unavailable.
>>> But if you simply have no output files, then you have no ability to
>>> restart.
>>>
>>> Mark
>>>
>>> On Tue, Sep 17, 2013 at 1:59 AM, Mahboobeh Eslami
>>>  wrote:
 hi my friends

 please help me

 i did 20 ns simulation by gromacs 4.5.5 but the power was shut down near
 the end of the simulation
 How to restart the crashed run?

  in the gromacs.org following comment has been proposed

 mdrun -s topol.tpr -cpi state.cpt

 but i don't have state.cpt in my folder.

 I need urgent help
 Thank you very much

 --
 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/Search before posting!
 * Please don't post (un)subscribe requests to the list. Use the
 www interface or send it to gmx-users-requ...@gromacs.org.
 * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>> --
>> 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/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> --
>> 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/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> 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/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www

[gmx-users] Re: grompp for minimization: note & warning

Dear Justin

I used newer version of gromacs (4.6.1), but my problem was not solved.


Any help will highly appreciated.
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Fw: Fw: [gmx-users] How to restart the crashed run


dear mark 

thank you so much
Good luck

- Forwarded Message -
From: Mark Abraham 
To: Mahboobeh Eslami ; Discussion list for GROMACS 
users  
Sent: Tuesday, September 17, 2013 1:21 PM
Subject: Re: Fw: [gmx-users] How to restart the crashed run
 

mdrun -v -deffnm md -cpi md

IIRC the -cpi file is immune from -deffnm

Mark

On Tue, Sep 17, 2013 at 4:48 AM, Mahboobeh Eslami
 wrote:
> dear mark
>
> yes i do
> my comment for md run was following
>
>
> mdrun -v -deffnm md >& md.job &
>
> now what comment is true for restart?
> I've recently started working with the gromacs and i am not professional
>  thank you and best wishes for you
>
> - Forwarded Message -
> From: Mark Abraham 
> To: Mahboobeh Eslami ; Discussion list for 
> GROMACS users 
> Sent: Tuesday, September 17, 2013 12:23 PM
> Subject: Re: [gmx-users] How to restart the crashed run
>
>
> You named them last time you ran mdrun, either explicitly or with
> -deffnm. Do the same.
>
> Mark
>
> On Tue, Sep 17, 2013 at 3:19 AM, Mahboobeh Eslami
>  wrote:
>> when i use following  omment for restart
>>
>> mdrun -s md.tpr -cpi md.cpt
>> i get following error
>>
>> Output file appending has been requested,
>> but some output files listed in the checkpoint file md.cpt
>> are not present or are named differently by the current program:
>> output files present: md.log
>> output files not present or named differently: md.trr md.edr
>>
>>
>> but i have md.trr  and md.edr in my folder.
>>
>> thank you so much
>>
>>
>> - Forwarded Message -
>> From: Mark Abraham 
>> To: Discussion list for GROMACS users 
>> Sent: Tuesday, September 17, 2013 11:22 AM
>> Subject: Re: [gmx-users] How to restart the crashed run
>>
>>
>> Hi,
>>
>> Please keep discussion on the mailing list.
>>
>> If you have a .cpt file that is not called state.cpt, then you must
>> have asked for the checkpoint file to be named md.cpt in your original
>> mdrun command (e.g. with mdrun -cpo md). state.cpt is simply the
>> default filename (and mostly there is no reason to change that).
>> Simply use md.cpt, now that you have it :-)
>>
>> Mark
>>
>>
>> On Tue, Sep 17, 2013 at 2:49 AM, Mahboobeh Eslami
>>  wrote:
>>> I have md.cpt but I don't have restart my run
>>> What is the purpose of the state.cpt file?
>>> thank you so much
>>>
>>> From: Mark Abraham 
>>> To: Mahboobeh Eslami ; Discussion list for
>>> GROMACS users 
>>> Sent: Tuesday, September 17, 2013 9:36 AM
>>> Subject: Re: [gmx-users] How to restart the crashed run
>>>
>>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests
>>> the 3.x-era restart strategy when checkpoint files are unavailable.
>>> But if you simply have no output files, then you have no ability to
>>> restart.
>>>
>>> Mark
>>>
>>> On Tue, Sep 17, 2013 at 1:59 AM, Mahboobeh Eslami
>>>  wrote:
 hi my friends

 please help me

 i did 20 ns simulation by gromacs 4.5.5 but the power was shut down near
 the end of the simulation
 How to restart the crashed run?

  in the gromacs.org following comment has been proposed

 mdrun -s topol.tpr -cpi state.cpt

 but i don't have state.cpt in my folder.

 I need urgent help
 Thank you very much

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

Re: [gmx-users] Re: grompp for minimization: note & warning



On 9/17/13 5:03 AM, shahab shariati wrote:

Dear Justin

I used newer version of gromacs (4.6.1), but my problem was not solved.



You're still working with outdated software.  Please follow my suggestion of 
trying 4.6.3.  The larger issue, in the end, is the unphysical configuration of 
the drug in the membrane.  Independent of Gromacs version, that setup will 
always fail.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

==
--
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

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

Fw: Fw: [gmx-users] How to restart the crashed run

dear mark

will all my output write well after restart and are their names md?
will old my output reconstruct or will generate new output?

thank


- Forwarded Message -
From: Mahboobeh Eslami 
To: "gmx-users@gromacs.org"  
Sent: Tuesday, September 17, 2013 2:00 PM
Subject: Fw: Fw: [gmx-users] How to restart the crashed run
 




dear mark 

thank you so much
Good luck

- Forwarded Message -
From: Mark Abraham 
To: Mahboobeh Eslami ; Discussion list for GROMACS 
users  
Sent: Tuesday, September 17, 2013 1:21 PM
Subject: Re: Fw: [gmx-users] How to restart the crashed run
 

mdrun -v -deffnm md -cpi md

IIRC the -cpi file is immune from -deffnm

Mark

On Tue, Sep 17, 2013 at 4:48 AM, Mahboobeh Eslami
 wrote:
> dear mark
>
> yes i do
> my comment for md run was following
>
>
> mdrun -v -deffnm md >& md.job &
>
> now what comment is true for restart?
> I've recently started working with the gromacs and i am not professional
>  thank you and best
 wishes for you
>
> - Forwarded Message -
> From: Mark Abraham 
> To: Mahboobeh Eslami ; Discussion list for 
> GROMACS users 
> Sent: Tuesday, September 17, 2013 12:23 PM
> Subject: Re: [gmx-users] How to restart the crashed run
>
>
> You named them last time you ran mdrun, either explicitly or with
> -deffnm. Do the same.
>
> Mark
>
> On Tue, Sep 17, 2013 at 3:19 AM, Mahboobeh Eslami
>  wrote:
>> when i use following  omment for restart
>>
>> mdrun -s md.tpr -cpi md.cpt
>> i get following error
>>
>> Output file appending has been requested,
>> but some output files listed in the checkpoint file md.cpt
>> are not present or are named differently by the current program:
>> output files present: md.log
>> output files not present or named differently: md.trr md.edr
>>
>>
>> but i have md.trr  and md.edr in my folder.
>>
>> thank you so much
>>
>>
>> - Forwarded Message -
>> From: Mark Abraham 
>> To: Discussion list for GROMACS users 
>> Sent: Tuesday, September 17, 2013 11:22 AM
>> Subject: Re: [gmx-users] How to restart the crashed run
>>
>>
>> Hi,
>>
>> Please keep discussion on the mailing list.
>>
>> If you have a .cpt file that is not called state.cpt, then you must
>> have asked for the checkpoint file to be named md.cpt in your original
>> mdrun command (e.g. with mdrun -cpo md). state.cpt is simply the
>> default filename (and mostly there is no reason to change that).
>> Simply use md.cpt, now that you have it :-)
>>
>> Mark
>>
>>
>> On Tue, Sep 17, 2013 at 2:49 AM, Mahboobeh Eslami
>>  wrote:
>>> I have md.cpt but I don't have restart my run
>>> What is the purpose of the state.cpt file?
>>> thank you so much
>>>
>>> From: Mark Abraham 
>>> To: Mahboobeh Eslami ; Discussion list for
>>> GROMACS users 
>>> Sent: Tuesday, September 17, 2013 9:36 AM
>>> Subject: Re: [gmx-users] How to restart the crashed run
>>>
>>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests
>>> the 3.x-era restart strategy when checkpoint files are unavailable.
>>> But if you simply have no output files, then you have no ability to
>>> restart.
>>>
>>> Mark
>>>
>>> On Tue, Sep 17, 2013 at 1:59 AM, Mahboobeh Eslami
>>>  wrote:
 hi my friends

 please help me

 i did 20 ns simulation by gromacs 4.5.5 but the power was shut down near
 the end of the simulation
 How to restart the crashed run?

  in
 the gromacs.org following comment has been proposed

 mdrun -s topol.tpr -cpi state.cpt

 but i don't have state.cpt in my folder.

 I need urgent help
 Thank you very much

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

Re: Fw: Fw: [gmx-users] How to restart the crashed run



On 9/17/13 5:58 AM, Mahboobeh Eslami wrote:

dear mark

will all my output write well after restart and are their names md?
will old my output reconstruct or will generate new output?



The default behavior of mdrun is to append to existing files.  Otherwise, you 
can use -noappend to get a new set of files that can be concatenated later.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

==
--
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

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

[gmx-users] g_analyze

2013-09-17 Thread afsaneh maleki

Dear all

When I use the following command:

g_analyze   -ffree_bi_0.9.xvg  -av  average_0.9

I got

set   average  standard  deviation   *std. dev.  /
sqrt(n-1)*…

SS16.053822e+01 3.062230e+01  1.936724e-02…

What is “*std. dev.  / sqrt(n-1)” *?

I know that

Standard deviation (SD) for samples is quall to sqrt[{sum((x-xmean)*2)/n-1}]

Standard error* *(SE) = Standard deviation/sqrt( n)

n is number of samples.

But I don’t know what is the concept of the “*std. dev.  / sqrt(n-1)”*?  is
it SE?



Sincerely

Afsaneh
--
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: grompp for minimization: note & warning

Dear Justin

Thanks for your reply


> You're still working with outdated software.  Please follow my
> suggestion of trying 4.6.3.

I try to install 4.6.3.

> The larger issue, in the end, is the unphysical configuration of the drug
> in the membrane.  Independent of Gromacs version, that setup will
> always fail.

I did minimization in 2 other states:

1) without drug (only membrane: DOPC nad cholesterol).

2) with drug but, this time, I put drug into water molecules not into
membrane.

Then I did mdrun for both of states. In both of state, there are not
following issues:

Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is
larger than the 1-4 table size 2.200 nm These are ignored for the rest of
the simulation This usually means your system is exploding,

if not, you should increase table-extension in your mdp file
or with user tables increase the table size

step 23: Water molecule starting at atom 10613 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

--
There are following outputs:

for state 1)
-

Reading file em.tpr, VERSION 4.5.1 (single precision)
Starting 4 threads
Making 2D domain decomposition 1 x 2 x 2

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=5

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 881 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  2.1828770e+05
Maximum force =  1.3656898e+04 on atom 618
Norm of force =  5.1748779e+02


for state 2)


Reading file em.tpr, VERSION 4.5.1 (single precision)
Starting 4 threads
Making 2D domain decomposition 1 x 2 x 2

Back Off! I just backed up em.trr to ./#em.trr.1#

Back Off! I just backed up em.edr to ./#em.edr.1#

Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=5

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Back Off! I just backed up em.gro to ./#em.gro.1#

Steepest Descents converged to machine precision in 845 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  1.9664772e+05
Maximum force =  1.0986521e+04 on atom 241
Norm of force =  4.4174323e+02
---

When I see created gro file from minimization (em.gro), I see some dopc and
cholesterol molecules were broken and they devided 2 or 3 parts. Input gro
file (system.gro) has 1835 residues. Created gro file from minimization
(em.gro) has 1835 residues. But when I load em.gro file in VMD, there are
1950 residues in graphical representation --> selections --> residues part.

Can I deduce my problem has not dependent to presence of drug?

Are there problem about my force field parameters or topology file ?

I get force field parameters from lipid book (for dopc and cholesterol) and
from prodrg server (for drug).

Please help me to resolve this issue.

Best wishes for you
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] A charge group moved too far between two domain decomposition steps

2013-09-17 Thread mabbasi

Dear All users


used OPLS ff for my system
After md production i get this error:

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated

How to solve the problem ??

Thank you




maryam abbasi, PhD student of Medicinal Chemistry
Department of Medicinal Chemistry,
Faculty of Pharmacy and Pharmaceutical Sciences (http;//pharm.mui.ac.ir/)
Isfahan University of Medical Sciences (http://www.mui.ac.ir), 
Hezar Jerib Ave. 
Isfahan, 
I.R.IRAN

-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: grompp for minimization: note & warning



On 9/17/13 7:02 AM, shahab shariati wrote:

Dear Justin

Thanks for your reply



You're still working with outdated software.  Please follow my
suggestion of trying 4.6.3.


I try to install 4.6.3.


The larger issue, in the end, is the unphysical configuration of the drug
in the membrane.  Independent of Gromacs version, that setup will
always fail.


I did minimization in 2 other states:

1) without drug (only membrane: DOPC nad cholesterol).

2) with drug but, this time, I put drug into water molecules not into
membrane.

Then I did mdrun for both of states. In both of state, there are not
following issues:

Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is
larger than the 1-4 table size 2.200 nm These are ignored for the rest of
the simulation This usually means your system is exploding,

if not, you should increase table-extension in your mdp file
or with user tables increase the table size

step 23: Water molecule starting at atom 10613 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

--
There are following outputs:

for state 1)
-

Reading file em.tpr, VERSION 4.5.1 (single precision)
Starting 4 threads
Making 2D domain decomposition 1 x 2 x 2

Steepest Descents:
Tolerance (Fmax)   =  1.0e+03
Number of steps=5

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 881 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  2.1828770e+05
Maximum force =  1.3656898e+04 on atom 618
Norm of force =  5.1748779e+02




As I suggested before, visualize the output file and figure out what is around 
atom 618 to cause such forces.



for state 2)


Reading file em.tpr, VERSION 4.5.1 (single precision)
Starting 4 threads
Making 2D domain decomposition 1 x 2 x 2

Back Off! I just backed up em.trr to ./#em.trr.1#

Back Off! I just backed up em.edr to ./#em.edr.1#

Steepest Descents:
Tolerance (Fmax)   =  1.0e+03
Number of steps=5

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Back Off! I just backed up em.gro to ./#em.gro.1#

Steepest Descents converged to machine precision in 845 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  1.9664772e+05
Maximum force =  1.0986521e+04 on atom 241
Norm of force =  4.4174323e+02
---



Same advice as above.


When I see created gro file from minimization (em.gro), I see some dopc and
cholesterol molecules were broken and they devided 2 or 3 parts. Input gro
file (system.gro) has 1835 residues. Created gro file from minimization
(em.gro) has 1835 residues. But when I load em.gro file in VMD, there are
1950 residues in graphical representation --> selections --> residues part.



What VMD thinks is a fragment, molecule, or residue is basically irrelevant. 
It's guessing based on guessing connectivity.  Your topology is definitive; VMD 
is not.



Can I deduce my problem has not dependent to presence of drug?



There seem to be problems in both cases.  Solve the issue with the membrane 
first.


Are there problem about my force field parameters or topology file ?

I get force field parameters from lipid book (for dopc and cholesterol) and
from prodrg server (for drug).



PRODRG generates notoriously bad parameters, particularly the charges.  See 
http://pubs.acs.org/doi/abs/10.1021/ci100335w.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

==
--
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't pos

Re: [gmx-users] A charge group moved too far between two domain decomposition steps

On 9/17/13 7:26 AM, mabbasi wrote:

Dear All users

used OPLS ff for my system
After md production i get this error:

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated

How to solve the problem ??

Start by taking mdrun's advice and referring to the Gromacs website, which has a
page describing most (if not all) of the common errors. Surely you would have
found this:

http://www.gromacs.org/Documentation/Errors#A_charge_group_moved_too_far_between_two_domain_decomposition_steps.

Beyond that, search the list archive, as these types of errors get posted and
solved daily. Among those thousands of threads, I'm sure something will be useful.

If you still need help, we can't do anything but guess at the problem without:

1. a complete description of what your system is
2. any new molecules or parameters you may have introduced
3. your protocol for building, minimizing, and equilibrating the system (the
outcome of EM is particularly important)

4. your complete .mdp file for the run that crashes

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

==
--
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.

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

[gmx-users] Re: grompp for minimization: note & warning

Dear Justin

Thanks for your time and consideration.

> As I suggested before, visualize the output file and figure out what is
> around atom 618 to cause such forces.

I visualized output file (em.gro) by VMD. Atom 618 is  belonged to a dopc
molecule (this dopc molecule is intact and is not broken). There are other
dopc and cholesterol molecules around atom 618. How I understand what
around this atom cause such forces.
Excuse me. Please give me more explanation about your suggestion.
May be, I did not understand your mean truly.
Should I remove this dopc molecule and then run minimization again?

> PRODRG generates notoriously bad parameters, particularly the charges.

I know this issue, charges and charges groups obtained from prodrg (in itp
file) were compared with charges and charges groups in similar structures
being in rtp file of gromos (because my drug is very similar to cytosine).
Then I corrected them.
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: grompp for minimization: note & warning



On 9/17/13 8:17 AM, shahab shariati wrote:

Dear Justin

Thanks for your time and consideration.


As I suggested before, visualize the output file and figure out what is
around atom 618 to cause such forces.


I visualized output file (em.gro) by VMD. Atom 618 is  belonged to a dopc
molecule (this dopc molecule is intact and is not broken). There are other
dopc and cholesterol molecules around atom 618. How I understand what
around this atom cause such forces.
Excuse me. Please give me more explanation about your suggestion.


Usually when large forces arise, the cause is fairly obvious.  There will be 
some atom very close to the one on which the maximum force acts.  It may not 
always be obvious.



May be, I did not understand your mean truly.
Should I remove this dopc molecule and then run minimization again?



No.


PRODRG generates notoriously bad parameters, particularly the charges.


I know this issue, charges and charges groups obtained from prodrg (in itp
file) were compared with charges and charges groups in similar structures
being in rtp file of gromos (because my drug is very similar to cytosine).
Then I corrected them.



OK, that's a reasonable starting point.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

==
--
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

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

[gmx-users] Re: grompp for minimization: note & warning

Dear Justin

Very very thanks for your quick reply.

I am very confused and amazed.

After visualization of atom 618 ( where the maximum force is),
what should I do to resolve me problem.

Any help will highly appreciated.
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: grompp for minimization: note & warning



On 9/17/13 8:47 AM, shahab shariati wrote:

Dear Justin

Very very thanks for your quick reply.

I am very confused and amazed.

After visualization of atom 618 ( where the maximum force is),
what should I do to resolve me problem.

Any help will highly appreciated.



I honestly have no idea.  There's something nasty going on there, but only you 
have the ability to see it.  You can always try a smaller value of emstep, a 
different EM algorithm, etc.  Try setting nstxout = 1 and visualize the entire 
EM "trajectory" to see where things start to go out of control.  And finally, if 
it really isn't working, ask the people who provided the coordinates - they're 
supposed to be pre-equilibrated, so if you can't get it to minimize, maybe 
there's something wrong that's happened before you even got your hands on the file.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

==
--
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

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

Re: [gmx-users] Constraining a part of the system

2013-09-17 Thread rahul seth

Thanks


On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul  wrote:

>
>
> On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:
>
>> Is there a way to constraint bonds of a part of the system while keeping
>> the other part flexible? For example for a simulation with two proteins, I
>> would like to constraint the bonds of one and would like to keep the other
>> flexible.
>>
>> I would prefer to use LINCS to constraint the system
>>
>>
> Set the constraints explicitly in the topology of one protein using a
> [constraints] directive.  Then set "constraints = none" in the .mdp file.
>  The constraints read from the topology will override the .mdp setting
> while leaving all other bonds unconstrained.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> 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
>
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Constraining a part of the system

Is there a way to constraint bonds of a part of the system while keeping
the other part flexible? For example for a simulation with two proteins, I
would like to constraint the bonds of one and would like to keep the other
flexible.

I would prefer to use LINCS to constraint the system
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Constraining a part of the system



On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:

Is there a way to constraint bonds of a part of the system while keeping
the other part flexible? For example for a simulation with two proteins, I
would like to constraint the bonds of one and would like to keep the other
flexible.

I would prefer to use LINCS to constraint the system



Set the constraints explicitly in the topology of one protein using a 
[constraints] directive.  Then set "constraints = none" in the .mdp file.  The 
constraints read from the topology will override the .mdp setting while leaving 
all other bonds unconstrained.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

==
--
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

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

RE: [gmx-users] g_current

2013-09-17 Thread Florian Dommert

Hi Nilesh,

 I looked at the code and was not able to find a reasonable condition, where
the last column of the mc output can contain -inf.
The only thing where the normalization would produce something like this is,
when the number of frames (nfr) equals the counter in the loop i for the
integral calculation. However this is a while loop with the condition
while(i -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Nilesh Dhumal
> Sent: Sunday, September 08, 2013 11:55 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] g_current
> 
> Did you get chance to take look at the g_current?
> 
> why it is -inf  (infinity)  at the end with -mc option (mc.xvg).
> >
> >
> >> -Original Message-
> >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> >> boun...@gromacs.org] On Behalf Of Nilesh Dhumal
> >> Sent: Tuesday, July 09, 2013 5:06 AM
> >> To: Discussion list for GROMACS users
> >> Subject: RE: [gmx-users] g_current
> >>
> >> Thanks for reply.
> >>
> >> Still I have a question why it is -inf  (infinity)  at the end.
> >
> > This is a good question. At the moment, the only thing I can imagine is
a
> > faulty normalization, because the value of the integral at t=0 equals
> > always
> > zero. However, if you integrate the first row with another tool, such as
> > g_analyze for example, the same values as in the second row show appear.
> >
> > As soon as I have some time left, I will take a look at the code and
> > report
> > back.
> >
> > /Flo
> >
> >>
> >> Nilesh
> >>
> >> > Hi,
> >> >
> >> >  I would say the problem is too less statistics. In the paper where
> >> the
> >> > tool
> >> > was introduced, a simulation of 100ns has been performed in order to
> >> > achieved sufficient sampling.
> >> >
> >> > The order of magnitude is given due to the units.
> >> >
> >> > Simulate for a longer time to get rid of the noise. Calculating these
> > kind
> >> > of correlations functions is really not a simple task.
> >> >
> >> > Schroeder et al. have published an article about fitting of
dielectric
> >> > spectra for ionic liquids, where this problem is discussed in detail.
> >> >
> >> > Cheers,
> >> > Flo
> >> >
> >> >> -Original Message-
> >> >> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> >> >> boun...@gromacs.org] On Behalf Of Nilesh Dhumal
> >> >> Sent: Monday, July 08, 2013 10:32 PM
> >> >> To: gmx-users@gromacs.org
> >> >> Subject: [gmx-users] g_current
> >> >>
> >> >> Hello,
> >> >> I am calculating the correlation of rotational and translation
dipole
> >> >> moment of ionic liquids. I run the 1 ns simulation and saved the
> >> >> trajectory at 1 fs.
> >> >>
> >> >> g_current -f md.trr -s md.tpr -n index.ndx -mc
> >> >>
> >> >> I selected "system" group.
> >> >>
> >> >> Here I pasted the initial j(t) vales and the final value is
infinity.
> >> >>
> >> >> # This file was created Sun Jul  7 20:51:59 2013
> >> >> # by the following command:
> >> >> # g_current -f md.trr -s md.tpr -e 10.0 -mc
> >> >> #
> >> >> # g_current is part of G R O M A C S:
> >> >> #
> >> >> # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
> >> >> #
> >> >> @title "M\sD\N - current  autocorrelation function"
> >> >> @xaxis  label "Time (ps)"
> >> >> @yaxis  label "< M\sD\N (0)\c7\CJ(t) >  (e nm/ps)\S2"
> >> >> @TYPE xy
> >> >> # time   M_D(0) J(t) acf Integral acf
> >> >> 0.000   -5.20584e-15 0
> >> >> 0.001   -6.97466e-15-1.42702e-17
> >> >> 0.002   -6.97511e-15-5.25081e-17
> >> >> 0.003   -6.97474e-15-9.07484e-17
> >> >> 0.004   -6.97391e-15-1.28987e-16
> >> >>
> >> >>
> >> >>
> >> >> Why final value is infinity? If I do autocorrelation function of
> >> these
> >> >> values, I get all values 0.
> >> >>
> >> >> Why J(t)values are in range of e-15?
> >> >>
> >> >> Nilesh
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> 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/Search before posting!
> >> >> * Please don't post (un)subscribe requests to the list. Use the
> >> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
> >> > --
> >> > 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/Search before posting!
> >> > * Please don't post (un)subscribe requests to the list. Use the
> >> > www interface or send it to gmx-users-requ...@gromacs.org.
> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
> >>
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> * Please search the archive at
> >> http://www

Re: [gmx-users] Regarding g_sgangle index file

2013-09-17 Thread Teemu Murtola

Hello,

Please keep correspondence on the list so that others may benefit from it,
and you don't need to wait for some particular person to respond.

On Tue, Sep 17, 2013 at 1:24 PM, Venkat Reddy  wrote:
>
> On Tue, Sep 17, 2013 at 12:38 AM, Teemu Murtola 
>>  wrote:
>>
>>> version (from the git master branch), you can use a much more powerful
>>> 'gmx
>>> gangle' tool, which can calculate multiple angles in one go.
>>>
>>
> I have installed the "gromacs-master" version from GIT, but I couldn't see
> any changes between the old g_sgangle and the current one. Is the new tool
> underway in development?
>

Try "gmx gangle -h" per my original suggestion. The g_sgangle tool hasn't
been touched.

Best regards,
Teemu
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] grompp for minimization: note & warning

Dear Justin

I did minimization with the newest version of gromacs (4.6.3).

But, unfortunately, problem was not solved.

Best wishes for you.
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] modify nsteps in an existing tpr file

2013-09-17 Thread Guanglei Cui

Dear GMX users,

I'm new to Gromacs. So apologies if this question is too simple.

I downloaded top/tpr files from the supplementary material of a published
paper. The nsteps set in the tpr file is 100ns. I wish to do a small test
run. Is there any way I can modify that? I've tried to create a mdp file
that best matches the parameters found through gmxdump, but it gives me a
lot of LINCS error. I can upload the mdp file and gmxdump file if you are
kind to help. Thanks in advance.

Best regards,
-- 
Guanglei Cui
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] modify nsteps in an existing tpr file

mdrun -nsteps in 4.6 overrides the number of steps in the .tpr

Mark

On Tue, Sep 17, 2013 at 8:55 PM, Guanglei Cui
 wrote:
> Dear GMX users,
>
> I'm new to Gromacs. So apologies if this question is too simple.
>
> I downloaded top/tpr files from the supplementary material of a published
> paper. The nsteps set in the tpr file is 100ns. I wish to do a small test
> run. Is there any way I can modify that? I've tried to create a mdp file
> that best matches the parameters found through gmxdump, but it gives me a
> lot of LINCS error. I can upload the mdp file and gmxdump file if you are
> kind to help. Thanks in advance.
>
> Best regards,
> --
> Guanglei Cui
> --
> 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/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Constraining a part of the system



On 9/17/13 4:50 PM, HANNIBAL LECTER wrote:

Is there a smart way of writing the constraint sections in the topology
file other than entering the values manually ?



Write a script that parses the [bonds] directive of the post-processed topology 
(output by grompp -pp) and write the relevant fields to a [constraints] directive.


-Justin



On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
wrote:


Thanks


On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul  wrote:




On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:


Is there a way to constraint bonds of a part of the system while keeping
the other part flexible? For example for a simulation with two

proteins, I

would like to constraint the bonds of one and would like to keep the

other

flexible.

I would prefer to use LINCS to constraint the system



Set the constraints explicitly in the topology of one protein using a
[constraints] directive.  Then set "constraints = none" in the .mdp file.
  The constraints read from the topology will override the .mdp setting
while leaving all other bonds unconstrained.

-Justin

--
==**

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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<

http://lists.gromacs.org/mailman/listinfo/gmx-users>

* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Search<

http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!

* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<

http://www.gromacs.org/Support/Mailing_Lists>



--
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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

==
--
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

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

Re: [gmx-users] Constraining a part of the system

@Vitaly. Yes you are right. However, I noticed that if I do not constraint
the bonds in my CNT my simulations run fine. It is indeed surprising to me
but I do not have much experience with simulating CNTs and if not
constraining the bonds seem to get things done, I think it is a viable
option. But still need to test a lot of things before I can decide on the
final settings.


On Tue, Sep 17, 2013 at 5:11 PM, HANNIBAL LECTER  wrote:

> Yes. That is the way to go about it. I was hoping for a more lazy
> approach... Thanks anyways.
>
>
> On Tue, Sep 17, 2013 at 5:07 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 9/17/13 4:50 PM, HANNIBAL LECTER wrote:
>>
>>> Is there a smart way of writing the constraint sections in the topology
>>> file other than entering the values manually ?
>>>
>>>
>> Write a script that parses the [bonds] directive of the post-processed
>> topology (output by grompp -pp) and write the relevant fields to a
>> [constraints] directive.
>>
>> -Justin
>>
>>
>>
>>> On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
>>> **wrote:
>>>
>>>  Thanks


 On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul 
 wrote:


>
> On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:
>
>  Is there a way to constraint bonds of a part of the system while
>> keeping
>> the other part flexible? For example for a simulation with two
>>
> proteins, I

> would like to constraint the bonds of one and would like to keep the
>>
> other

> flexible.
>>
>> I would prefer to use LINCS to constraint the system
>>
>>
>>  Set the constraints explicitly in the topology of one protein using a
> [constraints] directive.  Then set "constraints = none" in the .mdp
> file.
>   The constraints read from the topology will override the .mdp setting
> while leaving all other bonds unconstrained.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> 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
>
> ==
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> <
>
 http://lists.gromacs.org/**mailman/listinfo/gmx-users
 >

> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<
>
 http://www.gromacs.org/**Support/Mailing_Lists/Search
 >**before posting!

> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/Support/Mailing_Lists
> <
>
 http://www.gromacs.org/**Support/Mailing_Lists
 >

>
>  --
 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


>> --
>> ==**
>>
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> 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

Re: [gmx-users] Constraining a part of the system

Yes. That is the way to go about it. I was hoping for a more lazy
approach... Thanks anyways.


On Tue, Sep 17, 2013 at 5:07 PM, Justin Lemkul  wrote:

>
>
> On 9/17/13 4:50 PM, HANNIBAL LECTER wrote:
>
>> Is there a smart way of writing the constraint sections in the topology
>> file other than entering the values manually ?
>>
>>
> Write a script that parses the [bonds] directive of the post-processed
> topology (output by grompp -pp) and write the relevant fields to a
> [constraints] directive.
>
> -Justin
>
>
>
>> On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
>> **wrote:
>>
>>  Thanks
>>>
>>>
>>> On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul  wrote:
>>>
>>>

 On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:

  Is there a way to constraint bonds of a part of the system while
> keeping
> the other part flexible? For example for a simulation with two
>
 proteins, I
>>>
 would like to constraint the bonds of one and would like to keep the
>
 other
>>>
 flexible.
>
> I would prefer to use LINCS to constraint the system
>
>
>  Set the constraints explicitly in the topology of one protein using a
 [constraints] directive.  Then set "constraints = none" in the .mdp
 file.
   The constraints read from the topology will override the .mdp setting
 while leaving all other bonds unconstrained.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow

 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

 ==

 --
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
 <

>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>>> >
>>>
 * Please search the archive at http://www.gromacs.org/**
 Support/Mailing_Lists/Search<

>>> http://www.gromacs.org/**Support/Mailing_Lists/Search
>>> >**before posting!
>>>
 * Please don't post (un)subscribe requests to the list. Use the www
 interface or send it to gmx-users-requ...@gromacs.org.
 * Can't post? Read 
 http://www.gromacs.org/Support/Mailing_Lists
 <

>>> http://www.gromacs.org/**Support/Mailing_Lists
>>> >
>>>

  --
>>> 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
>>>
>>>
> --
> ==**
>
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> 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
>
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] modify nsteps in an existing tpr file

2013-09-17 Thread Guanglei Cui

Thanks. Is it possible to dump the parameters in the tpr file to a mdp file?


On Tue, Sep 17, 2013 at 3:20 PM, Mark Abraham wrote:

> mdrun -nsteps in 4.6 overrides the number of steps in the .tpr
>
> Mark
>
> On Tue, Sep 17, 2013 at 8:55 PM, Guanglei Cui
>  wrote:
> > Dear GMX users,
> >
> > I'm new to Gromacs. So apologies if this question is too simple.
> >
> > I downloaded top/tpr files from the supplementary material of a published
> > paper. The nsteps set in the tpr file is 100ns. I wish to do a small test
> > run. Is there any way I can modify that? I've tried to create a mdp file
> > that best matches the parameters found through gmxdump, but it gives me a
> > lot of LINCS error. I can upload the mdp file and gmxdump file if you are
> > kind to help. Thanks in advance.
> >
> > Best regards,
> > --
> > Guanglei Cui
> > --
> > 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/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> 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/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Guanglei Cui
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Constraining a part of the system

Is there a smart way of writing the constraint sections in the topology
file other than entering the values manually ?


On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
wrote:

> Thanks
>
>
> On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:
> >
> >> Is there a way to constraint bonds of a part of the system while keeping
> >> the other part flexible? For example for a simulation with two
> proteins, I
> >> would like to constraint the bonds of one and would like to keep the
> other
> >> flexible.
> >>
> >> I would prefer to use LINCS to constraint the system
> >>
> >>
> > Set the constraints explicitly in the topology of one protein using a
> > [constraints] directive.  Then set "constraints = none" in the .mdp file.
> >  The constraints read from the topology will override the .mdp setting
> > while leaving all other bonds unconstrained.
> >
> > -Justin
> >
> > --
> > ==**
> >
> > Justin A. Lemkul, Ph.D.
> > Postdoctoral Fellow
> >
> > 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<
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > * Please search the archive at http://www.gromacs.org/**
> > Support/Mailing_Lists/Search<
> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > * Please don't post (un)subscribe requests to the list. Use the www
> > interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> http://www.gromacs.org/Support/Mailing_Lists>
> >
> --
> 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/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] BGQ compilation with verlet kernels: #include file "kernel_impl.h" not found.

2013-09-17 Thread Christopher Neale

Dear Users:

I am attempting to use the new BGQ kernels with the version of gromacs at 
https://gerrit.gromacs.org/#/c/2572/ , which I obtained by:

git init
git fetch https://gerrit.gromacs.org/gromacs refs/changes/72/2572/1 && git 
checkout FETCH_HEAD

I then attempted to compile like this:

module purge
module load vacpp/12.1 xlf/14.1 mpich2/xl
module load cmake/2.8.8
module load fftw/3.3.2
export FFTW_LOCATION=/scinet/bgq/Libraries/fftw-3.3.2
cmake ../source/ \
  -DCMAKE_PREFIX_PATH=$FFTW_LOCATION \
  -DCMAKE_INSTALL_PREFIX=$(pwd) \
  -DGMX_X11=OFF \
  -DGMX_MPI=OFF \
  -DGMX_PREFER_STATIC_LIBS=ON 
make -j 4
make install

###

That gave me the following error during make:

Scanning dependencies of target gromacs_include_links
[  0%] Generating gromacs
[  0%] Built target gromacs_include_links
Scanning dependencies of target gmx
[  0%] [  0%] [  0%] [  0%] [  0%] [  0%] [  0%] [  0%] [  1%] Building C 
object src/gmxlib/CMakeFiles/gmx.dir/gmxcpp.c.o
[  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/md_logging.c.o
Building C object src/gmxlib/CMakeFiles/gmx.dir/vmddlopen.c.o
[  1%] [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/chargegroup.c.o
Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_cpuid.c.o
[  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_rw.c.o
Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio.c.o
[  1%] [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trxio.c.o
[  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_system_xdr.c.o
Building C object src/gmxlib/CMakeFiles/gmx.dir/wgms.c.o
Building C object src/gmxlib/CMakeFiles/gmx.dir/wman.c.o
Building C object src/gmxlib/CMakeFiles/gmx.dir/smalloc.c.o
Building C object src/gmxlib/CMakeFiles/gmx.dir/rmpbc.c.o
Building C object src/gmxlib/CMakeFiles/gmx.dir/nrjac.c.o
Building C object src/gmxlib/CMakeFiles/gmx.dir/index.c.o
Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_thread_affinity.c.o
[  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mshift.c.o
[  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/macros.c.o
[  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/oenv.c.o
[  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/maths.c.o
[  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_omp.c.o
[  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/random.c.o
[  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_sort.c.o
[  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_random.c.o
[  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/md5.c.o
[  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/network.c.o
[  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/copyrite.c.o
[  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/cinvsqrtdata.c.o
[  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/writeps.c.o
[  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mtop_util.c.o
"/home/p/pomes/cneale/exec/gromacs-4.6.3_bgq/source/src/gmxlib/network.c", line 
264.10: 1506-296 (S) #include file  not found.
make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/network.c.o] Error 1
make[2]: *** Waiting for unfinished jobs
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
make: *** [all] Error 2

###

After some looking around, I added the following line before cmake:

export CFLAGS=-I/bgsys/drivers/ppcfloor

That solved the initial problem, but now I have the following error:

...
[  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/writeps.c.o
[  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mtop_util.c.o
[  3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_fatal.c.o
"/bgsys/drivers/ppcfloor/spi/include/kernel/location.h", line 34.10: 1506-296 
(S) #include file "kernel_impl.h" not found.
"/bgsys/drivers/ppcfloor/spi/include/kernel/process.h", line 36.10: 1506-296 
(S) #include file "kernel_impl.h" not found.
"/bgsys/drivers/ppcfloor/spi/include/kernel/process.h", line 194.10: 1506-296 
(S) #include file "process_impl.h" not found.
"/bgsys/drivers/ppcfloor/spi/include/kernel/location.h", line 173.10: 1506-296 
(S) #include file "location_impl.h" not found.
make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/network.c.o] Error 1
make[2]: *** Waiting for unfinished jobs
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
make: *** [all] Error 2

###

And it's harder to know what to do now since there are multiple instances of 
kernel_impl.h , etc.:

bgqdev-fen1-$ find /bgsys/drivers/ppcfloor/spi/include/kernel/|grep 
kernel_impl.h
/bgsys/drivers/ppcfloor/spi/include/kernel/cnk/kernel_impl.h
/bgsys/drivers/ppcfloor/spi/include/kernel/firmware/kernel_impl.h
/bgsys/drivers/ppcfloor/spi/include/kernel/klinux/kernel_impl.h


Does this indicate that the computer that I am using really has such a 
non-standard BG/Q setup? or is it possible that compiling on the BG/Q with the 
new verlet kernel requires an entirely different approach?

I understand that the Jenkins Buildbot has succes

Re: [gmx-users] Constraining a part of the system

2013-09-17 Thread Dr. Vitaly Chaban

the smart way is to constrain everything at once in MDP...
Dr. Vitaly V. Chaban


On Tue, Sep 17, 2013 at 10:50 PM, HANNIBAL LECTER
 wrote:
> Is there a smart way of writing the constraint sections in the topology
> file other than entering the values manually ?
>
>
> On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
> wrote:
>
>> Thanks
>>
>>
>> On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul  wrote:
>>
>> >
>> >
>> > On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:
>> >
>> >> Is there a way to constraint bonds of a part of the system while keeping
>> >> the other part flexible? For example for a simulation with two
>> proteins, I
>> >> would like to constraint the bonds of one and would like to keep the
>> other
>> >> flexible.
>> >>
>> >> I would prefer to use LINCS to constraint the system
>> >>
>> >>
>> > Set the constraints explicitly in the topology of one protein using a
>> > [constraints] directive.  Then set "constraints = none" in the .mdp file.
>> >  The constraints read from the topology will override the .mdp setting
>> > while leaving all other bonds unconstrained.
>> >
>> > -Justin
>> >
>> > --
>> > ==**
>> >
>> > Justin A. Lemkul, Ph.D.
>> > Postdoctoral Fellow
>> >
>> > 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<
>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> > * Please search the archive at http://www.gromacs.org/**
>> > Support/Mailing_Lists/Search<
>> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> > * Please don't post (un)subscribe requests to the list. Use the www
>> > interface or send it to gmx-users-requ...@gromacs.org.
>> > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
>> http://www.gromacs.org/Support/Mailing_Lists>
>> >
>> --
>> 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/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
> --
> 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/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] BGQ compilation with verlet kernels: #include file "kernel_impl.h" not found.

On Tue, Sep 17, 2013 at 5:31 PM, Christopher Neale
 wrote:
> Dear Users:
>
> I am attempting to use the new BGQ kernels with the version of gromacs at 
> https://gerrit.gromacs.org/#/c/2572/ , which I obtained by:
>
> git init
> git fetch https://gerrit.gromacs.org/gromacs refs/changes/72/2572/1 && git 
> checkout FETCH_HEAD
>
> I then attempted to compile like this:
>
> module purge
> module load vacpp/12.1 xlf/14.1 mpich2/xl
> module load cmake/2.8.8
> module load fftw/3.3.2
> export FFTW_LOCATION=/scinet/bgq/Libraries/fftw-3.3.2
> cmake ../source/ \
>   -DCMAKE_PREFIX_PATH=$FFTW_LOCATION \
>   -DCMAKE_INSTALL_PREFIX=$(pwd) \
>   -DGMX_X11=OFF \
>   -DGMX_MPI=OFF \

It's theoretically possible to make use of non-MPI mdrun on BG/Q, but
I've never tried it and wouldn't encourage it. What's your objective?
I'd be closer to prohibiting a thread-MPI or serial build on
BlueGene/Q than to doing work to make it possible.

>   -DGMX_PREFER_STATIC_LIBS=ON
> make -j 4
> make install
>
> ###
>
> That gave me the following error during make:
>
> Scanning dependencies of target gromacs_include_links
> [  0%] Generating gromacs
> [  0%] Built target gromacs_include_links
> Scanning dependencies of target gmx
> [  0%] [  0%] [  0%] [  0%] [  0%] [  0%] [  0%] [  0%] [  1%] Building C 
> object src/gmxlib/CMakeFiles/gmx.dir/gmxcpp.c.o
> [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/md_logging.c.o
> Building C object src/gmxlib/CMakeFiles/gmx.dir/vmddlopen.c.o
> [  1%] [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/chargegroup.c.o
> Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_cpuid.c.o
> [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio_rw.c.o
> Building C object src/gmxlib/CMakeFiles/gmx.dir/gmxfio.c.o
> [  1%] [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trxio.c.o
> [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_system_xdr.c.o
> Building C object src/gmxlib/CMakeFiles/gmx.dir/wgms.c.o
> Building C object src/gmxlib/CMakeFiles/gmx.dir/wman.c.o
> Building C object src/gmxlib/CMakeFiles/gmx.dir/smalloc.c.o
> Building C object src/gmxlib/CMakeFiles/gmx.dir/rmpbc.c.o
> Building C object src/gmxlib/CMakeFiles/gmx.dir/nrjac.c.o
> Building C object src/gmxlib/CMakeFiles/gmx.dir/index.c.o
> Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_thread_affinity.c.o
> [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mshift.c.o
> [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/macros.c.o
> [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/oenv.c.o
> [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/maths.c.o
> [  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_omp.c.o
> [  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/random.c.o
> [  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_sort.c.o
> [  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_random.c.o
> [  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/md5.c.o
> [  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/network.c.o
> [  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/copyrite.c.o
> [  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/cinvsqrtdata.c.o
> [  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/writeps.c.o
> [  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mtop_util.c.o
> "/home/p/pomes/cneale/exec/gromacs-4.6.3_bgq/source/src/gmxlib/network.c", 
> line 264.10: 1506-296 (S) #include file  not 
> found.

Hmm. That #include is taken from the BG/Q Application Development
manual, to set up the query you can see in
https://gerrit.gromacs.org/#/c/2572/1/src/gmxlib/network.c. I expected
it to Just Work, but it seems that code assumes MPI.

> make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/network.c.o] Error 1
> make[2]: *** Waiting for unfinished jobs
> make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
> make: *** [all] Error 2
>
> ###
>
> After some looking around, I added the following line before cmake:
>
> export CFLAGS=-I/bgsys/drivers/ppcfloor
>
> That solved the initial problem, but now I have the following error:
>
> ...
> [  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/writeps.c.o
> [  2%] Building C object src/gmxlib/CMakeFiles/gmx.dir/mtop_util.c.o
> [  3%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_fatal.c.o
> "/bgsys/drivers/ppcfloor/spi/include/kernel/location.h", line 34.10: 1506-296 
> (S) #include file "kernel_impl.h" not found.
> "/bgsys/drivers/ppcfloor/spi/include/kernel/process.h", line 36.10: 1506-296 
> (S) #include file "kernel_impl.h" not found.
> "/bgsys/drivers/ppcfloor/spi/include/kernel/process.h", line 194.10: 1506-296 
> (S) #include file "process_impl.h" not found.
> "/bgsys/drivers/ppcfloor/spi/include/kernel/location.h", line 173.10: 
> 1506-296 (S) #include file "location_impl.h" not found.
> make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/network.c.o] Error 1
> make[2]: *** Waiting for unfinished jobs
> make[1]: *** [src/g

Re: [gmx-users] modify nsteps in an existing tpr file

No. Theoretically useful, but not implemented.

Mark

On Tue, Sep 17, 2013 at 4:45 PM, Guanglei Cui
 wrote:
> Thanks. Is it possible to dump the parameters in the tpr file to a mdp file?
>
>
> On Tue, Sep 17, 2013 at 3:20 PM, Mark Abraham wrote:
>
>> mdrun -nsteps in 4.6 overrides the number of steps in the .tpr
>>
>> Mark
>>
>> On Tue, Sep 17, 2013 at 8:55 PM, Guanglei Cui
>>  wrote:
>> > Dear GMX users,
>> >
>> > I'm new to Gromacs. So apologies if this question is too simple.
>> >
>> > I downloaded top/tpr files from the supplementary material of a published
>> > paper. The nsteps set in the tpr file is 100ns. I wish to do a small test
>> > run. Is there any way I can modify that? I've tried to create a mdp file
>> > that best matches the parameters found through gmxdump, but it gives me a
>> > lot of LINCS error. I can upload the mdp file and gmxdump file if you are
>> > kind to help. Thanks in advance.
>> >
>> > Best regards,
>> > --
>> > Guanglei Cui
>> > --
>> > 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/Search before posting!
>> > * Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-requ...@gromacs.org.
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> --
>> 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/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Guanglei Cui
> --
> 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/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Constraining a part of the system

Does anyone have proper parameters for CNTs ? I have been trying to perform
Simulations with finite CNTs. However, none of the parameters so far
(obtained from literature) seem to give the output temperatures equal to
set temperatures.

I have been looked into my input files time and again, but I could not
locate any bug so far. The problem is if I simulate my CNT with bonds
angles dihedrals and 1-4 interactions and constraint the bonds, the
temperature of the CNT seems to deviate far from the set temperature with
reasonable values of tau-t using the sd integrator in GROMACS.

Does anyone have parameters for CNTs such that they work with the SD
integrator with reasonable tau-t values?


On Tue, Sep 17, 2013 at 5:14 PM, HANNIBAL LECTER  wrote:

> @Vitaly. Yes you are right. However, I noticed that if I do not constraint
> the bonds in my CNT my simulations run fine. It is indeed surprising to me
> but I do not have much experience with simulating CNTs and if not
> constraining the bonds seem to get things done, I think it is a viable
> option. But still need to test a lot of things before I can decide on the
> final settings.
>
>
> On Tue, Sep 17, 2013 at 5:11 PM, HANNIBAL LECTER <
> hanniballecte...@gmail.com> wrote:
>
>> Yes. That is the way to go about it. I was hoping for a more lazy
>> approach... Thanks anyways.
>>
>>
>> On Tue, Sep 17, 2013 at 5:07 PM, Justin Lemkul  wrote:
>>
>>>
>>>
>>> On 9/17/13 4:50 PM, HANNIBAL LECTER wrote:
>>>
 Is there a smart way of writing the constraint sections in the topology
 file other than entering the values manually ?


>>> Write a script that parses the [bonds] directive of the post-processed
>>> topology (output by grompp -pp) and write the relevant fields to a
>>> [constraints] directive.
>>>
>>> -Justin
>>>
>>>
>>>
 On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
 **wrote:

  Thanks
>
>
> On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul 
> wrote:
>
>
>>
>> On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:
>>
>>  Is there a way to constraint bonds of a part of the system while
>>> keeping
>>> the other part flexible? For example for a simulation with two
>>>
>> proteins, I
>
>> would like to constraint the bonds of one and would like to keep the
>>>
>> other
>
>> flexible.
>>>
>>> I would prefer to use LINCS to constraint the system
>>>
>>>
>>>  Set the constraints explicitly in the topology of one protein using
>> a
>> [constraints] directive.  Then set "constraints = none" in the .mdp
>> file.
>>   The constraints read from the topology will override the .mdp
>> setting
>> while leaving all other bonds unconstrained.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> 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
>>
>> ==
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> <
>>
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> >
>
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<
>>
> http://www.gromacs.org/**Support/Mailing_Lists/Search
> >**before posting!
>
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read 
>> http://www.gromacs.org/Support/Mailing_Lists
>> <
>>
> http://www.gromacs.org/**Support/Mailing_Lists
> >
>
>>
>>  --
> 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
>
>
>>> --
>>> ==**
>>>
>>

[gmx-users] BGQ compilation with verlet kernels: #include file "kernel_impl.h" not found.

2013-09-17 Thread Christopher Neale

Indeed, it works just fine when I compile with mpi. I never thought to check 
that. My usual procedure is
to compile the whole package without mpi and then to compile mdrun with mpi. 
Thanks for the help Mark.

Here is the compilation script that worked for me.

module purge
module load vacpp/12.1 xlf/14.1 mpich2/xl
module load cmake/2.8.8
module load fftw/3.3.2

export FFTW_LOCATION=/scinet/bgq/Libraries/fftw-3.3.2

cmake ../source/ \
  -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \
  -DCMAKE_PREFIX_PATH=$FFTW_LOCATION \
  -DCMAKE_INSTALL_PREFIX=$(pwd) \
  -DGMX_X11=OFF \
  -DGMX_MPI=ON \
  -DGMX_PREFER_STATIC_LIBS=ON

make -j 16
make install

--
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/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] changing atom types versus adding dihedrals to atom types

2013-09-17 Thread Rafael I. Silverman y de la Vega

Can you give some examples of how these verifications are  different for
different force fields? It doesnt seem like verifying takes that much time,
but a theorist prof in my department told me not to worry as long as my
system doesnt blow up...
And what do you mean "thourough parametrization?
I parametrized flavin mononucleotide using amber99sb-ildn, I used existing
atomtypes in the force field, but I added partial atomic charges based on a
decent DFT calculation in orca, and I had to add 2 distance restraints on
the delta negatively charged phosphate oxygens to keep them from crashing
into the delta positive hydrogen on the same phosphate. Is that thorough in
your opinion?
Thanks

On Thu, Sep 12, 2013 at 7:32 PM, Justin Lemkul  wrote:

>
>
> On 9/12/13 7:04 PM, Rafael I. Silverman y de la Vega wrote:
>
>> I see,
>>   when you say thorough parametrization and validation, what do you mean?
>> How does one validate the system, calculate free energy in solution and
>> compare it to tabulated data?
>>
>>
> The target data depend on the force field for which parameters are being
> developed.  Matching QM geometries, water interaction energies and
> distances, free energies of solvation, crystal structures, liquid
> properties, etc. are all useful depending on the underlying force field and
> how it was derived.  For bonded parameters, matching QM energy scans and/or
> vibrational properties are common.
>
> -Justin
>
>
>> On Wed, Sep 11, 2013 at 4:57 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 9/11/13 6:07 PM, Rafael I. Silverman y de la Vega wrote:
>>>
>>>  Hi all,
 in another thread it was recommended that instead of changing the atom
 types by analogy to ones with the desired parameter already assigned,
 that
 instead one should assign bonded parameters by analogy.  I was just
 wondering how this is better?


>>> I didn't suggest that.  I said that any assignment by analogy can have
>>> negative outcomes.  Bonds and angles, in theory, are a bit easier to deal
>>> with because the nonbonded interactions between their atoms are excluded.
>>>   Torsions are very difficult because the torsional bonded terms have to
>>> be
>>> balanced against the charge and LJ parameters of atoms separated by 3
>>> bonds, i.e. 1-4 interactions.
>>>
>>> Let me state very clearly that, for any missing parameters, anything
>>> short
>>> of a thorough parametrization and validation is (in my purist mind)
>>> unsound.
>>>
>>>
>>> As long as the atom type isnt too different, then why would the
>>> torsions
>>>
 not work out right? If the parameters are interrelated, what makes it
 better to add one term to an atom type rather than changing all the
 terms
 (to ones that are supposed to be together)?


  The key is being sufficiently similar, but even subtle differences
>>> between
>>> LJ parameters have very large consequences, especially for 1-4
>>> interactions, so I find it hard to believe that one will recapitulate
>>> accurate interactions in this case.  Of course, all assignments by
>>> analogy
>>> bear some penalty for nonequivalent groups.  I balked at your initial
>>> post
>>> in the other thread because there was no need to mess with atom types.
>>>  The
>>> system at hand there contained protein and lipid and could be completely
>>> described by existing atom types and bonded types, the OP there was just
>>> (and perhaps still is) constructing the force field incorrectly.  I felt
>>> it
>>> need to be stated that the approach there would not necessarily be
>>> productive, and to make sure the archive was complete so that no one
>>> would
>>> come across a post in vacuum and assume that he or she can simply swap
>>> around atom types to make error messages go away.  Your initial statement
>>> referred only to bonds and angles, which indeed would be insensitive to
>>> changes in LJ parameters on any of those atoms, but since the thread was
>>> in
>>> the context of dihedrals, I thought I should state my opinion there.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> 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
>>>
>>> ==
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search>> Mailing_Lists/Search>before
>>> posting!
>>>
>>> * Please don't post (un)subscribe requests to

Re: [gmx-users] changing atom types versus adding dihedrals to atom types