from:"Elsaid Younes"

Re: [gmx-users] Gromacs installation.

2016-05-19 Thread Elsaid Younes

 http://gerrit.gromacs.org/download/regressiontests-5.0.4.tar.gz
I think that something makes this link not downloadable. When I disable the
download from -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON by
deleting -DREGRESSIONTEST_DOWNLOAD=ON asking me to
make GMX_BUILD_UNITTESTS=ON
Then after I made it, I still get this
Total Test time (real) = 165.57 sec
[100%] Built target run-ctest
[100%] Unit tests disabled
NOTE: Unit tests have not been run. You need to set GMX_BUILD_UNITTESTS=ON
if you want to build and run them.
[100%] Built target unittests-notice
[100%] Built target check..After all Gromacs can not start.

On Fri, May 13, 2016 at 12:53 PM, Elsaid Younes <elk...@gmail.com> wrote:

> Hi all,
>
> I have installed gromacs like the quick and dirty installation. I have a
> 16.04 version of ubuntu. I can not start it.
> I used to do the same procedure in ubuntu 15.10, and it worked fine.
>
> /Elsaid
>
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[gmx-users] Gromacs installation.

2016-05-13 Thread Elsaid Younes

Hi all,

I have installed gromacs like the quick and dirty installation. I have a
16.04 version of ubuntu. I can not start it.
I used to do the same procedure in ubuntu 15.10, and it worked fine.

/Elsaid
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Re: [gmx-users] Extend the simulation

2016-02-22 Thread Elsaid Younes

Hi,
I have two inquiries:

1-I got this error message:
Fatal error:
Checksum wrong for 'md_0_1.log'. The file has been replaced or its contents
have been modified. Cannot do appending because of this condition.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


2-I would like to know the meaning of this message:

Received the TERM signal, stopping at the next NS step


 Average load imbalance: 11.7 %
 Part of the total run time spent waiting due to load imbalance: 0.4 %
 Average PME mesh/force load: 1.080
 Part of the total run time spent waiting due to PP/PME imbalance: 4.4 %


   Core t (s)   Wall t (s)(%)
   Time:   197934.452   198048.563   99.9
 2d07h00:48
 (ns/day)(hour/ns)
Performance:5.5544.321


/Elsaid

On Sun, Feb 21, 2016 at 3:56 AM, Elsaid Younes <elk...@gmail.com> wrote:

> Sorry
> Once, I added .tpr to the md_0_1 then it gave me the above message then I
> did as you said without .tpr.
> That error was obtained:
>
> Fatal error:
> Can't read 509132 bytes of 'md_0_1.log' to compute checksum. The file has
> been replaced or its contents have been modified. Cannot do appending
> because of this condition.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> /Elsaid
>
> On Sun, Feb 21, 2016 at 3:38 AM, Elsaid Younes <elk...@gmail.com> wrote:
>
>> It says:
>>
>> No previous checkpoint file present, assuming this is a new run.
>> Reading file md_0_1.tpr, VERSION 5.0.4 (single precision)
>> Changing nstlist from 10 to 20, rlist from 1 to 1.03
>>
>> then start..
>>
>> /Elsaid
>>
>> On Sun, Feb 21, 2016 at 3:21 AM, Elsaid Younes <elk...@gmail.com> wrote:
>>
>>> Ok, How can I use md_0_1.tpr instead of topol.tpr
>>>
>>> /Elsaid
>>>
>>> On Sun, Feb 21, 2016 at 2:59 AM, Elsaid Younes <elk...@gmail.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> The mdrun I did was gmx mdrun -deffnm md_0_1
>>>> I write the command
>>>>  mdrun -cpi md_0_1_prev.cpt -append
>>>>  I tried to use -noappend, but still doesn't work.
>>>>
>>>> /Elsaid
>>>>
>>>> On Sun, Feb 21, 2016 at 2:43 AM, Elsaid Younes <elk...@gmail.com>
>>>> wrote:
>>>>
>>>>> Still asks for topol.tpr? Can I have that file
>>>>>
>>>>>
>>>>> /Elsaid
>>>>> On 2/20/16 6:49 PM, Elsaid Younes wrote:
>>>>> >* Hi,
>>>>> *>>>* If I have this file md_0_1_prev.cpt What is the text exactly? It 
>>>>> asks
>>>>> *>* for topol.tpr
>>>>> *
>>>>> I gave you the command-line options that are new to the mdrun command 
>>>>> line.  Run
>>>>> whatever mdrun you did before, but add -cpi -append.  Doing this is a 
>>>>> routine
>>>>> task, covered on the website and in half a million posts in the archive 
>>>>> (Google
>>>>> is your friend).
>>>>>
>>>>> -Justin
>>>>>
>>>>> >* On 2/20/16 5:32 PM, Elsaid wrote:
>>>>> *>>* * The simulation has the time,  which is time of the wanted 
>>>>> simulation. But the
>>>>> *>* *>* job was killed by the server.
>>>>> *>* *
>>>>> *>* If the simulation terminated prior to completion, you don't need to 
>>>>> operate on
>>>>> *>* the .tpr file at all.  Just continue from the last checkpoint
>>>>> *>>* mdrun -cpi -append
>>>>> *>>* -Justin*
>>>>>
>>>>>
>>>>> On Sun, Feb 21, 2016 at 1:49 AM, Elsaid Younes <elk...@gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>>
>>>>>> If I have this file md_0_1_prev.cpt What is the text exactly? It asks 
>>>>>> for topol.tpr
>>>>>> On 2/20/16 5:32 PM, Elsaid wrote:
>>>>>> >* The simulation has the time,  which is time of the wanted simulation. 
>>>>>> >But the
>>>>>> *>* job was killed by the server.
>>>>>> *
>>>>>> If the sim

Re: [gmx-users] Extend the simulation

2016-02-20 Thread Elsaid Younes

Sorry
Once, I added .tpr to the md_0_1 then it gave me the above message then I
did as you said without .tpr.
That error was obtained:

Fatal error:
Can't read 509132 bytes of 'md_0_1.log' to compute checksum. The file has
been replaced or its contents have been modified. Cannot do appending
because of this condition.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

/Elsaid

On Sun, Feb 21, 2016 at 3:38 AM, Elsaid Younes <elk...@gmail.com> wrote:

> It says:
>
> No previous checkpoint file present, assuming this is a new run.
> Reading file md_0_1.tpr, VERSION 5.0.4 (single precision)
> Changing nstlist from 10 to 20, rlist from 1 to 1.03
>
> then start..
>
> /Elsaid
>
> On Sun, Feb 21, 2016 at 3:21 AM, Elsaid Younes <elk...@gmail.com> wrote:
>
>> Ok, How can I use md_0_1.tpr instead of topol.tpr
>>
>> /Elsaid
>>
>> On Sun, Feb 21, 2016 at 2:59 AM, Elsaid Younes <elk...@gmail.com> wrote:
>>
>>> Hi,
>>>
>>> The mdrun I did was gmx mdrun -deffnm md_0_1
>>> I write the command
>>>  mdrun -cpi md_0_1_prev.cpt -append
>>>  I tried to use -noappend, but still doesn't work.
>>>
>>> /Elsaid
>>>
>>> On Sun, Feb 21, 2016 at 2:43 AM, Elsaid Younes <elk...@gmail.com> wrote:
>>>
>>>> Still asks for topol.tpr? Can I have that file
>>>>
>>>>
>>>> /Elsaid
>>>> On 2/20/16 6:49 PM, Elsaid Younes wrote:
>>>> >* Hi,
>>>> *>>>* If I have this file md_0_1_prev.cpt What is the text exactly? It asks
>>>> *>* for topol.tpr
>>>> *
>>>> I gave you the command-line options that are new to the mdrun command 
>>>> line.  Run
>>>> whatever mdrun you did before, but add -cpi -append.  Doing this is a 
>>>> routine
>>>> task, covered on the website and in half a million posts in the archive 
>>>> (Google
>>>> is your friend).
>>>>
>>>> -Justin
>>>>
>>>> >* On 2/20/16 5:32 PM, Elsaid wrote:
>>>> *>>* * The simulation has the time,  which is time of the wanted 
>>>> simulation. But the
>>>> *>* *>* job was killed by the server.
>>>> *>* *
>>>> *>* If the simulation terminated prior to completion, you don't need to 
>>>> operate on
>>>> *>* the .tpr file at all.  Just continue from the last checkpoint
>>>> *>>* mdrun -cpi -append
>>>> *>>* -Justin*
>>>>
>>>>
>>>> On Sun, Feb 21, 2016 at 1:49 AM, Elsaid Younes <elk...@gmail.com>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>>
>>>>> If I have this file md_0_1_prev.cpt What is the text exactly? It asks for 
>>>>> topol.tpr
>>>>> On 2/20/16 5:32 PM, Elsaid wrote:
>>>>> >* The simulation has the time,  which is time of the wanted simulation. 
>>>>> >But the
>>>>> *>* job was killed by the server.
>>>>> *
>>>>> If the simulation terminated prior to completion, you don't need to 
>>>>> operate on
>>>>> the .tpr file at all.  Just continue from the last checkpoint
>>>>>
>>>>> mdrun -cpi -append
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 629
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>> jalemkul at outerbanks.umaryland.edu 
>>>>> <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> | 
>>>>> (410) 706-7441http://mackerell.umaryland.edu/~jalemkul
>>>>>
>>>>>
>>>>>
>>>>> On Sun, Feb 21, 2016 at 12:32 AM, Elsaid <elk...@gmail.com> wrote:
>>>>>
>>>>>> The simulation has the time,  which is time of the wanted simulation.
>>>>>> But the job was killed by the server.
>>>>>> /Elsaid
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
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Re: [gmx-users] Extend the simulation

2016-02-20 Thread Elsaid Younes

It says:

No previous checkpoint file present, assuming this is a new run.
Reading file md_0_1.tpr, VERSION 5.0.4 (single precision)
Changing nstlist from 10 to 20, rlist from 1 to 1.03

then start..

/Elsaid

On Sun, Feb 21, 2016 at 3:21 AM, Elsaid Younes <elk...@gmail.com> wrote:

> Ok, How can I use md_0_1.tpr instead of topol.tpr
>
> /Elsaid
>
> On Sun, Feb 21, 2016 at 2:59 AM, Elsaid Younes <elk...@gmail.com> wrote:
>
>> Hi,
>>
>> The mdrun I did was gmx mdrun -deffnm md_0_1
>> I write the command
>>  mdrun -cpi md_0_1_prev.cpt -append
>>  I tried to use -noappend, but still doesn't work.
>>
>> /Elsaid
>>
>> On Sun, Feb 21, 2016 at 2:43 AM, Elsaid Younes <elk...@gmail.com> wrote:
>>
>>> Still asks for topol.tpr? Can I have that file
>>>
>>>
>>> /Elsaid
>>> On 2/20/16 6:49 PM, Elsaid Younes wrote:
>>> >* Hi,
>>> *>>>* If I have this file md_0_1_prev.cpt What is the text exactly? It asks
>>> *>* for topol.tpr
>>> *
>>> I gave you the command-line options that are new to the mdrun command line. 
>>>  Run
>>> whatever mdrun you did before, but add -cpi -append.  Doing this is a 
>>> routine
>>> task, covered on the website and in half a million posts in the archive 
>>> (Google
>>> is your friend).
>>>
>>> -Justin
>>>
>>> >* On 2/20/16 5:32 PM, Elsaid wrote:
>>> *>>* * The simulation has the time,  which is time of the wanted 
>>> simulation. But the
>>> *>* *>* job was killed by the server.
>>> *>* *
>>> *>* If the simulation terminated prior to completion, you don't need to 
>>> operate on
>>> *>* the .tpr file at all.  Just continue from the last checkpoint
>>> *>>* mdrun -cpi -append
>>> *>>* -Justin*
>>>
>>>
>>> On Sun, Feb 21, 2016 at 1:49 AM, Elsaid Younes <elk...@gmail.com> wrote:
>>>
>>>> Hi,
>>>>
>>>>
>>>> If I have this file md_0_1_prev.cpt What is the text exactly? It asks for 
>>>> topol.tpr
>>>> On 2/20/16 5:32 PM, Elsaid wrote:
>>>> >* The simulation has the time,  which is time of the wanted simulation. 
>>>> >But the
>>>> *>* job was killed by the server.
>>>> *
>>>> If the simulation terminated prior to completion, you don't need to 
>>>> operate on
>>>> the .tpr file at all.  Just continue from the last checkpoint
>>>>
>>>> mdrun -cpi -append
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 629
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>> jalemkul at outerbanks.umaryland.edu 
>>>> <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> | 
>>>> (410) 706-7441http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>>
>>>>
>>>> On Sun, Feb 21, 2016 at 12:32 AM, Elsaid <elk...@gmail.com> wrote:
>>>>
>>>>> The simulation has the time,  which is time of the wanted simulation.
>>>>> But the job was killed by the server.
>>>>> /Elsaid
>>>>>
>>>>
>>>>
>>>
>>
>
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Re: [gmx-users] Extend the simulation

2016-02-20 Thread Elsaid Younes

Ok, How can I use md_0_1.tpr instead of topol.tpr

/Elsaid

On Sun, Feb 21, 2016 at 2:59 AM, Elsaid Younes <elk...@gmail.com> wrote:

> Hi,
>
> The mdrun I did was gmx mdrun -deffnm md_0_1
> I write the command
>  mdrun -cpi md_0_1_prev.cpt -append
>  I tried to use -noappend, but still doesn't work.
>
> /Elsaid
>
> On Sun, Feb 21, 2016 at 2:43 AM, Elsaid Younes <elk...@gmail.com> wrote:
>
>> Still asks for topol.tpr? Can I have that file
>>
>>
>> /Elsaid
>> On 2/20/16 6:49 PM, Elsaid Younes wrote:
>> >* Hi,
>> *>>>* If I have this file md_0_1_prev.cpt What is the text exactly? It asks
>> *>* for topol.tpr
>> *
>> I gave you the command-line options that are new to the mdrun command line.  
>> Run
>> whatever mdrun you did before, but add -cpi -append.  Doing this is a routine
>> task, covered on the website and in half a million posts in the archive 
>> (Google
>> is your friend).
>>
>> -Justin
>>
>> >* On 2/20/16 5:32 PM, Elsaid wrote:
>> *>>* * The simulation has the time,  which is time of the wanted simulation. 
>> But the
>> *>* *>* job was killed by the server.
>> *>* *
>> *>* If the simulation terminated prior to completion, you don't need to 
>> operate on
>> *>* the .tpr file at all.  Just continue from the last checkpoint
>> *>>* mdrun -cpi -append
>> *>>* -Justin*
>>
>>
>> On Sun, Feb 21, 2016 at 1:49 AM, Elsaid Younes <elk...@gmail.com> wrote:
>>
>>> Hi,
>>>
>>>
>>> If I have this file md_0_1_prev.cpt What is the text exactly? It asks for 
>>> topol.tpr
>>> On 2/20/16 5:32 PM, Elsaid wrote:
>>> >* The simulation has the time,  which is time of the wanted simulation. 
>>> >But the
>>> *>* job was killed by the server.
>>> *
>>> If the simulation terminated prior to completion, you don't need to operate 
>>> on
>>> the .tpr file at all.  Just continue from the last checkpoint
>>>
>>> mdrun -cpi -append
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>> jalemkul at outerbanks.umaryland.edu 
>>> <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> | 
>>> (410) 706-7441http://mackerell.umaryland.edu/~jalemkul
>>>
>>>
>>>
>>> On Sun, Feb 21, 2016 at 12:32 AM, Elsaid <elk...@gmail.com> wrote:
>>>
>>>> The simulation has the time,  which is time of the wanted simulation.
>>>> But the job was killed by the server.
>>>> /Elsaid
>>>>
>>>
>>>
>>
>
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Re: [gmx-users] Extend the simulation

2016-02-20 Thread Elsaid Younes

Hi,

The mdrun I did was gmx mdrun -deffnm md_0_1
I write the command
 mdrun -cpi md_0_1_prev.cpt -append
 I tried to use -noappend, but still doesn't work.

/Elsaid

On Sun, Feb 21, 2016 at 2:43 AM, Elsaid Younes <elk...@gmail.com> wrote:

> Still asks for topol.tpr? Can I have that file
>
>
> /Elsaid
> On 2/20/16 6:49 PM, Elsaid Younes wrote:
> >* Hi,
> *>>>* If I have this file md_0_1_prev.cpt What is the text exactly? It asks
> *>* for topol.tpr
> *
> I gave you the command-line options that are new to the mdrun command line.  
> Run
> whatever mdrun you did before, but add -cpi -append.  Doing this is a routine
> task, covered on the website and in half a million posts in the archive 
> (Google
> is your friend).
>
> -Justin
>
> >* On 2/20/16 5:32 PM, Elsaid wrote:
> *>>* * The simulation has the time,  which is time of the wanted simulation. 
> But the
> *>* *>* job was killed by the server.
> *>* *
> *>* If the simulation terminated prior to completion, you don't need to 
> operate on
> *>* the .tpr file at all.  Just continue from the last checkpoint
> *>>* mdrun -cpi -append
> *>>* -Justin*
>
>
> On Sun, Feb 21, 2016 at 1:49 AM, Elsaid Younes <elk...@gmail.com> wrote:
>
>> Hi,
>>
>>
>> If I have this file md_0_1_prev.cpt What is the text exactly? It asks for 
>> topol.tpr
>> On 2/20/16 5:32 PM, Elsaid wrote:
>> >* The simulation has the time,  which is time of the wanted simulation. But 
>> >the
>> *>* job was killed by the server.
>> *
>> If the simulation terminated prior to completion, you don't need to operate 
>> on
>> the .tpr file at all.  Just continue from the last checkpoint
>>
>> mdrun -cpi -append
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> jalemkul at outerbanks.umaryland.edu 
>> <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> | (410) 
>> 706-7441http://mackerell.umaryland.edu/~jalemkul
>>
>>
>>
>> On Sun, Feb 21, 2016 at 12:32 AM, Elsaid <elk...@gmail.com> wrote:
>>
>>> The simulation has the time,  which is time of the wanted simulation.
>>> But the job was killed by the server.
>>> /Elsaid
>>>
>>
>>
>
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Re: [gmx-users] Extend the simulation

2016-02-20 Thread Elsaid Younes

Still asks for topol.tpr? Can I have that file


/Elsaid
On 2/20/16 6:49 PM, Elsaid Younes wrote:
>* Hi,
*>>>* If I have this file md_0_1_prev.cpt What is the text exactly? It asks
*>* for topol.tpr
*
I gave you the command-line options that are new to the mdrun command
line.  Run
whatever mdrun you did before, but add -cpi -append.  Doing this is a routine
task, covered on the website and in half a million posts in the archive (Google
is your friend).

-Justin

>* On 2/20/16 5:32 PM, Elsaid wrote:
*>>* * The simulation has the time,  which is time of the wanted
simulation. But the
*>* *>* job was killed by the server.
*>* *
*>* If the simulation terminated prior to completion, you don't need
to operate on
*>* the .tpr file at all.  Just continue from the last checkpoint
*>>* mdrun -cpi -append
*>>* -Justin*


On Sun, Feb 21, 2016 at 1:49 AM, Elsaid Younes <elk...@gmail.com> wrote:

> Hi,
>
>
> If I have this file md_0_1_prev.cpt What is the text exactly? It asks for 
> topol.tpr
> On 2/20/16 5:32 PM, Elsaid wrote:
> >* The simulation has the time,  which is time of the wanted simulation. But 
> >the
> *>* job was killed by the server.
> *
> If the simulation terminated prior to completion, you don't need to operate on
> the .tpr file at all.  Just continue from the last checkpoint
>
> mdrun -cpi -append
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu 
> <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> | (410) 
> 706-7441http://mackerell.umaryland.edu/~jalemkul
>
>
>
> On Sun, Feb 21, 2016 at 12:32 AM, Elsaid <elk...@gmail.com> wrote:
>
>> The simulation has the time,  which is time of the wanted simulation. But
>> the job was killed by the server.
>> /Elsaid
>>
>
>
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Re: [gmx-users] Extend the simulation

2016-02-20 Thread Elsaid Younes

Hi,

If I have this file md_0_1_prev.cpt What is the text exactly? It asks
for topol.tpr
On 2/20/16 5:32 PM, Elsaid wrote:
>* The simulation has the time,  which is time of the wanted simulation. But the
*>* job was killed by the server.
*
If the simulation terminated prior to completion, you don't need to operate on
the .tpr file at all.  Just continue from the last checkpoint

mdrun -cpi -append

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu
 |
(410) 706-7441http://mackerell.umaryland.edu/~jalemkul

On Sun, Feb 21, 2016 at 12:32 AM, Elsaid  wrote:

> The simulation has the time,  which is time of the wanted simulation. But
> the job was killed by the server.
> /Elsaid
>
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[gmx-users] Extend the simulation

2016-02-20 Thread Elsaid Younes

Hi all,

I need to extend a previous simulation, and its directory is the same with
all inputs and outpts. That simulation  can not be complete due to the
maximum time of the job which is limited by the server. I use gromacs 5,
when using the command gmx convert-tpr, an error is obtained.

Command line:
  gmx convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr


---
Program gmx, VERSION 5.0.4
Source code file:
/local/easybuild/build/GROMACS/5.0.4/intel-2016.01-mt/gromacs-5.0.4/src/gromacs/commandline/pargs.cpp,
line: 80

Fatal error:
Expected a real argument for option -extend

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---



Is that the only way to extend the simulation? The time of extension has
limits?

/Elsaid
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[gmx-users] Scripts to the gromacs

2016-01-04 Thread Elsaid Younes

Hey all,

I wish I can find a way to help me writing a script to the gromacs. I mean
by scripts "the commands that one writes to gramacs terminals and the
choices, which are prompted after command's processing, all collected in
one file"
I do simulation like lysozyme in water tutorial.
Looking forward to hearing from you!

Elsaid
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[gmx-users] X11 forwarding!

2015-12-15 Thread Elsaid Younes

Hi all,


I can not do ssh over X, although my sshd-config is:


# Package generated configuration file
# See the sshd_config(5) manpage for details

# What ports, IPs and protocols we listen for
Port 22
# Use these options to restrict which interfaces/protocols sshd will bind to
#ListenAddress ::
#ListenAddress 0.0.0.0
Protocol 2
# HostKeys for protocol version 2
HostKey /etc/ssh/ssh_host_rsa_key
HostKey /etc/ssh/ssh_host_dsa_key
HostKey /etc/ssh/ssh_host_ecdsa_key
HostKey /etc/ssh/ssh_host_ed25519_key
#Privilege Separation is turned on for security
UsePrivilegeSeparation yes

# Lifetime and size of ephemeral version 1 server key
KeyRegenerationInterval 3600
ServerKeyBits 1024

# Logging
SyslogFacility AUTH
LogLevel INFO

# Authentication:
LoginGraceTime 120
PermitRootLogin without-password
StrictModes yes

RSAAuthentication yes
PubkeyAuthentication yes
#AuthorizedKeysFile %h/.ssh/authorized_keys

# Don't read the user's ~/.rhosts and ~/.shosts files
IgnoreRhosts yes
# For this to work you will also need host keys in /etc/ssh_known_hosts
RhostsRSAAuthentication no
# similar for protocol version 2
HostbasedAuthentication no
# Uncomment if you don't trust ~/.ssh/known_hosts for RhostsRSAAuthentication
#IgnoreUserKnownHosts yes

# To enable empty passwords, change to yes (NOT RECOMMENDED)
PermitEmptyPasswords no

# Change to yes to enable challenge-response passwords (beware issues with
# some PAM modules and threads)
ChallengeResponseAuthentication no

# Change to no to disable tunnelled clear text passwords
#PasswordAuthentication yes

# Kerberos options
#KerberosAuthentication no
#KerberosGetAFSToken no
#KerberosOrLocalPasswd yes
#KerberosTicketCleanup yes

# GSSAPI options
#GSSAPIAuthentication no
#GSSAPICleanupCredentials yes
X11UseLocalHost no
X11Forwarding yes
X11DisplayOffset 10
PrintMotd no
PrintLastLog yes
TCPKeepAlive yes
#UseLogin no

#MaxStartups 10:30:60
#Banner /etc/issue.net

# Allow client to pass locale environment variables
AcceptEnv LANG LC_*

Subsystem sftp /usr/lib/openssh/sftp-server

# Set this to 'yes' to enable PAM authentication, account processing,
# and session processing. If this is enabled, PAM authentication will
# be allowed through the ChallengeResponseAuthentication and
# PasswordAuthentication.  Depending on your PAM configuration,
# PAM authentication via ChallengeResponseAuthentication may bypass
# the setting of "PermitRootLogin without-password".
# If you just want the PAM account and session checks to run without
# PAM authentication, then enable this but set PasswordAuthentication
# and ChallengeResponseAuthentication to 'no'.
UsePAM yes





Typing xauth info shows:

File new: yes
File locked:  no
Number of entries:0
Changes honored:  yes
Changes made: no
Current input:(argv):1

Also I can't use scp. Any ideas?
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[gmx-users] rm command.

2015-12-04 Thread Elsaid Younes

Hi,

Can anyone please tell me how to remove a file from directory?
rm doesn't work.
for example:
rm/prss/sss/topol.top
There are three files of it.

/Elsaid
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Re: [gmx-users] mpirun

2015-11-10 Thread Elsaid Younes

Hi,

I deleted the old one and moved another one using box.com since scp doesn't
work, but I got  the same results.
Any ideas?

/Elsaid

On Tue, Nov 10, 2015 at 3:02 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 11/9/15 7:59 PM, Elsaid Younes wrote:
>
>> Hi,
>>
>> it gives me file input/output  error 1aki.pdb.
>>
>>
> The most likely explanation is that file doesn't exist in the working
> directory.
>
> -Justin
>
>
> Elsaid
>>
>> On Mon, Nov 9, 2015 at 8:20 PM, Elsaid Younes <elk...@gmail.com> wrote:
>>
>> Thank you!
>>>
>>> On Mon, Nov 9, 2015 at 8:18 PM, Samuel Flores <samuelflor...@gmail.com>
>>> wrote:
>>>
>>> Oh that makes sense!
>>>>
>>>> Elsaid, issue:
>>>>
>>>>   module load gromacs/5.0.4
>>>>
>>>> "module load gromacs" defaults to an ancient release of gromacs.
>>>>
>>>> Sam
>>>>
>>>> On Nov 9, 2015, at 19:10, Justin Lemkul <jalem...@vt.edu> wrote:
>>>>>
>>>>>
>>>>>
>>>>> On 11/9/15 1:08 PM, Samuel Flores wrote:
>>>>>
>>>>>> Hi Justin,
>>>>>>
>>>>>> Is gmx the same as ngmx?  Here are the binaries in the Uppmax gromacs
>>>>>>
>>>>> directory:
>>>>
>>>>>
>>>>>>
>>>>> gmx refers to the single binary provided as of 5.0, which is the new
>>>>>
>>>> setup. What appears here is a (very) outdated version of GROMACS, and
>>>> usage
>>>> needs to be adjusted accordingly.
>>>>
>>>>>
>>>>> -Justin
>>>>>
>>>>> [samuelf@tintin1 ~]$ ls /sw/apps/gromacs/4.6.3/tintin/bin/
>>>>>> GMXRC g_anadock_d  g_cluster  g_densorder_d
>>>>>>
>>>>>   g_enemat   g_helixorient_d  g_morph  g_pme_error_d  g_rmsdist
>>>> g_select_d   g_trajgenbox  make_edi_d   trjcat_d
>>>>
>>>>> GMXRC.bashg_anaeig g_cluster_dg_dielectricg_enemat_d
>>>>>>
>>>>> g_hydorder   g_morph_dg_polystat g_rmsdist_d  g_sgangle
>>>> g_traj_d  genbox_dmake_ndx trjconv
>>>>
>>>>> GMXRC.csh g_anaeig_d   g_clustsizeg_dielectric_d  g_energy
>>>>>>
>>>>> g_hydorder_d g_msdg_polystat_d   g_rmsf
>>>>  g_sgangle_d
>>>> g_tune_pmegenconf make_ndx_d   trjconv_d
>>>>
>>>>> GMXRC.zsh g_analyzeg_clustsize_d  g_dipoles   g_energy_d
>>>>>>
>>>>> g_kinetics   g_msd_d  g_potentialg_rmsf_d g_sham
>>>>   g_tune_pme_d  genconf_d   mdruntrjorder
>>>>
>>>>> completion.bash  g_analyze_d  g_confrms  g_dipoles_d g_filter
>>>>>>
>>>>>g_kinetics_d g_nmeig  g_potential_d  g_rotacf
>>>>   g_sham_d g_vanhove genion  mdrun_d  trjorder_d
>>>>
>>>>> completion.cshg_angle  g_confrms_dg_disre
>>>>>>
>>>>>   g_filter_d g_lieg_nmeig_dg_principal
>>>> g_rotacf_d
>>>>   g_sigeps g_vanhove_d   genion_dmdrun_mpixplor2gmx.pl
>>>>
>>>>> completion.zshg_angle_dg_covarg_disre_d
>>>>>>
>>>>>   g_gyrate   g_lie_d  g_nmens  g_principal_d  g_rotmat
>>>>   g_sigeps_d   g_velacc  genrestrmdrun_mpi_d  xplor2gmx.pl~
>>>>
>>>>> demux.pl  g_barg_covar_d  g_dist  g_gyrate_d
>>>>>>
>>>>> g_luck   g_nmens_dg_protonateg_rotmat_d   g_sorient
>>>> g_velacc_dgenrestr_d  mk_angndxxpm2ps
>>>>
>>>>> do_dssp   g_bar_d  g_current  g_dist_d
>>>>>>
>>>>> g_h2order  g_luck_d g_nmtraj g_protonate_d  g_saltbr
>>>>   g_sorient_d  g_whamgmxcheckmk_angndx_d  xpm2ps_d
>>>>
>>>>> do_dssp_d g_bond   g_current_dg_dos   g_h2order_d
>>>>>>
>>>>>g_mdmat  g_nmtraj_d   g_rama g_saltbr_d   g_spatial
>>>> g_wham_d  gmxcheck_d  ngmx
>>>>
>>>>>

Re: [gmx-users] mpirun

2015-11-09 Thread Elsaid Younes

Thank you!

On Mon, Nov 9, 2015 at 8:18 PM, Samuel Flores <samuelflor...@gmail.com>
wrote:

> Oh that makes sense!
>
> Elsaid, issue:
>
>  module load gromacs/5.0.4
>
> "module load gromacs" defaults to an ancient release of gromacs.
>
> Sam
>
> > On Nov 9, 2015, at 19:10, Justin Lemkul <jalem...@vt.edu> wrote:
> >
> >
> >
> > On 11/9/15 1:08 PM, Samuel Flores wrote:
> >> Hi Justin,
> >>
> >> Is gmx the same as ngmx?  Here are the binaries in the Uppmax gromacs
> directory:
> >>
> >
> > gmx refers to the single binary provided as of 5.0, which is the new
> setup. What appears here is a (very) outdated version of GROMACS, and usage
> needs to be adjusted accordingly.
> >
> > -Justin
> >
> >> [samuelf@tintin1 ~]$ ls /sw/apps/gromacs/4.6.3/tintin/bin/
> >> GMXRC g_anadock_d  g_cluster  g_densorder_d
>  g_enemat   g_helixorient_d  g_morph  g_pme_error_d  g_rmsdist
> g_select_d   g_trajgenbox  make_edi_d   trjcat_d
> >> GMXRC.bashg_anaeig g_cluster_dg_dielectricg_enemat_d
>  g_hydorder   g_morph_dg_polystat g_rmsdist_d  g_sgangle
> g_traj_d  genbox_dmake_ndx trjconv
> >> GMXRC.csh g_anaeig_d   g_clustsizeg_dielectric_d  g_energy
>  g_hydorder_d g_msdg_polystat_d   g_rmsf   g_sgangle_d
> g_tune_pmegenconf make_ndx_d   trjconv_d
> >> GMXRC.zsh g_analyzeg_clustsize_d  g_dipoles   g_energy_d
>  g_kinetics   g_msd_d  g_potentialg_rmsf_d g_sham
>  g_tune_pme_d  genconf_d   mdruntrjorder
> >> completion.bash  g_analyze_d  g_confrms  g_dipoles_d g_filter
>   g_kinetics_d g_nmeig  g_potential_d  g_rotacf
>  g_sham_d g_vanhove genion  mdrun_d  trjorder_d
> >> completion.cshg_angle  g_confrms_dg_disre
>  g_filter_d g_lieg_nmeig_dg_principalg_rotacf_d
>  g_sigeps g_vanhove_d   genion_dmdrun_mpixplor2gmx.pl
> >> completion.zshg_angle_dg_covarg_disre_d
>  g_gyrate   g_lie_d  g_nmens  g_principal_d  g_rotmat
>  g_sigeps_d   g_velacc  genrestrmdrun_mpi_d  xplor2gmx.pl~
> >> demux.pl  g_barg_covar_d  g_dist  g_gyrate_d
>g_luck   g_nmens_dg_protonateg_rotmat_d   g_sorient
> g_velacc_dgenrestr_d  mk_angndxxpm2ps
> >> do_dssp   g_bar_d  g_current  g_dist_d
> g_h2order  g_luck_d g_nmtraj g_protonate_d  g_saltbr
>  g_sorient_d  g_whamgmxcheckmk_angndx_d  xpm2ps_d
> >> do_dssp_d g_bond   g_current_dg_dos   g_h2order_d
>   g_mdmat  g_nmtraj_d   g_rama g_saltbr_d   g_spatial
> g_wham_d  gmxcheck_d  ngmx
> >> editconf  g_bond_d g_density  g_dos_d g_hbond
>   g_mdmat_dg_optionsg_rama_d   g_sans   g_spatial_d
> g_wheel   gmxdump pdb2gmx
> >> editconf_dg_bundle g_density_dg_dyecoupl  g_hbond_d
>   g_membed g_options_d  g_rdf  g_sans_d g_spol
>  g_wheel_d gmxdump_d   pdb2gmx_d
> >> eneconv   g_bundle_d   g_densmap  g_dyecoupl_d
> g_helixg_membed_d   g_order  g_rdf_dg_sas
> g_spol_d g_x2top   grompp  tpbconv
> >> eneconv_d g_chig_densmap_dg_dyndomg_helix_d
>   g_mindistg_order_dg_rms  g_sas_d  g_tcaf
>  g_x2top_d grompp_dtpbconv_d
> >> g_anadock g_chi_d  g_densorderg_dyndom_d
> g_helixorient  g_mindist_d  g_pme_error  g_rms_dg_select
>  g_tcaf_d g_xrama   make_editrjcat
> >>
> >>
> >> Elsaid,
> >>
> >> Regarding Justin’s suggestion, on Uppmax I believe the full path would
> be:
> >>
> >> source  /sw/apps/gromacs/4.6.3/tintin/bin/GMXRC.bash
> >>
> >>
> >> However I think you already issued
> >>
> >> module load gromacs
> >>
> >> which might source GMXRC .
> >>
> >> Sam
> >>
> >>
> >>> On Nov 9, 2015, at 17:56, Justin Lemkul <jalem...@vt.edu> wrote:
> >>>
> >>>
> >>>
> >>> On 11/9/15 11:55 AM, Elsaid Younes wrote:
> >>>> Hi,
> >>>>
> >>>> Thank you for your response.
> >>>> When writing gmx, it gives the command not found. (Note I use windows)
> >&

Re: [gmx-users] mpirun

2015-11-09 Thread Elsaid Younes

Hi,

Thank you for your response.
When writing gmx, it gives the command not found. (Note I use windows)

Elsaid

On Mon, Nov 9, 2015 at 3:31 PM, Justin Lemkul  wrote:

>
>
> On 11/9/15 5:23 AM, Said wrote:
>
>> Hi,
>>
>> I have a gateway access to uppmax. I could have copied 1aki.pdb to my
>> account using box.com since scp does not work.
>>
>> when writing mpirun -np 1 pdb2gmx -f 1aki.pdb -o 1aki_processed.gro -water
>> spce,
>> it gives me an error with exit code: 225.
>>
>>
> There is not point trying to run pdb2gmx with mpirun; preparation steps
> should usually be done interactively, ideally on a local machine, and the
> .tpr file sent to the cluster to execute mdrun.  Most preparation programs
> need some kind of interactive input, which can be scripted but it is not
> always obvious what needs to be done ahead of time, especially something as
> complex as pdb2gmx.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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> * Please search the archive at
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> posting!
>
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Re: [gmx-users] mpirun

2015-11-09 Thread Elsaid Younes

Hi,

it gives me file input/output  error 1aki.pdb.

Elsaid

On Mon, Nov 9, 2015 at 8:20 PM, Elsaid Younes <elk...@gmail.com> wrote:

> Thank you!
>
> On Mon, Nov 9, 2015 at 8:18 PM, Samuel Flores <samuelflor...@gmail.com>
> wrote:
>
>> Oh that makes sense!
>>
>> Elsaid, issue:
>>
>>  module load gromacs/5.0.4
>>
>> "module load gromacs" defaults to an ancient release of gromacs.
>>
>> Sam
>>
>> > On Nov 9, 2015, at 19:10, Justin Lemkul <jalem...@vt.edu> wrote:
>> >
>> >
>> >
>> > On 11/9/15 1:08 PM, Samuel Flores wrote:
>> >> Hi Justin,
>> >>
>> >> Is gmx the same as ngmx?  Here are the binaries in the Uppmax gromacs
>> directory:
>> >>
>> >
>> > gmx refers to the single binary provided as of 5.0, which is the new
>> setup. What appears here is a (very) outdated version of GROMACS, and usage
>> needs to be adjusted accordingly.
>> >
>> > -Justin
>> >
>> >> [samuelf@tintin1 ~]$ ls /sw/apps/gromacs/4.6.3/tintin/bin/
>> >> GMXRC g_anadock_d  g_cluster  g_densorder_d
>>  g_enemat   g_helixorient_d  g_morph  g_pme_error_d  g_rmsdist
>> g_select_d   g_trajgenbox  make_edi_d   trjcat_d
>> >> GMXRC.bashg_anaeig g_cluster_dg_dielectricg_enemat_d
>>g_hydorder   g_morph_dg_polystat g_rmsdist_d  g_sgangle
>> g_traj_d  genbox_dmake_ndx trjconv
>> >> GMXRC.csh g_anaeig_d   g_clustsizeg_dielectric_d  g_energy
>>g_hydorder_d g_msdg_polystat_d   g_rmsf   g_sgangle_d
>> g_tune_pmegenconf make_ndx_d   trjconv_d
>> >> GMXRC.zsh g_analyzeg_clustsize_d  g_dipoles   g_energy_d
>>g_kinetics   g_msd_d  g_potentialg_rmsf_d g_sham
>>  g_tune_pme_d  genconf_d   mdruntrjorder
>> >> completion.bash  g_analyze_d  g_confrms  g_dipoles_d g_filter
>>   g_kinetics_d g_nmeig  g_potential_d  g_rotacf
>>  g_sham_d g_vanhove genion  mdrun_d  trjorder_d
>> >> completion.cshg_angle  g_confrms_dg_disre
>>  g_filter_d g_lieg_nmeig_dg_principalg_rotacf_d
>>  g_sigeps g_vanhove_d   genion_dmdrun_mpixplor2gmx.pl
>> >> completion.zshg_angle_dg_covarg_disre_d
>>  g_gyrate   g_lie_d  g_nmens  g_principal_d  g_rotmat
>>  g_sigeps_d   g_velacc  genrestrmdrun_mpi_d  xplor2gmx.pl~
>> >> demux.pl  g_barg_covar_d  g_dist  g_gyrate_d
>>g_luck   g_nmens_dg_protonateg_rotmat_d   g_sorient
>> g_velacc_dgenrestr_d  mk_angndxxpm2ps
>> >> do_dssp   g_bar_d  g_current  g_dist_d
>> g_h2order  g_luck_d g_nmtraj g_protonate_d  g_saltbr
>>  g_sorient_d  g_whamgmxcheckmk_angndx_d  xpm2ps_d
>> >> do_dssp_d g_bond   g_current_dg_dos   g_h2order_d
>>   g_mdmat  g_nmtraj_d   g_rama g_saltbr_d   g_spatial
>> g_wham_d  gmxcheck_d  ngmx
>> >> editconf  g_bond_d g_density  g_dos_d g_hbond
>>   g_mdmat_dg_optionsg_rama_d   g_sans   g_spatial_d
>> g_wheel   gmxdump pdb2gmx
>> >> editconf_dg_bundle g_density_dg_dyecoupl  g_hbond_d
>>   g_membed g_options_d  g_rdf  g_sans_d g_spol
>>  g_wheel_d gmxdump_d   pdb2gmx_d
>> >> eneconv   g_bundle_d   g_densmap  g_dyecoupl_d
>> g_helixg_membed_d   g_order  g_rdf_dg_sas
>> g_spol_d g_x2top   grompp  tpbconv
>> >> eneconv_d g_chig_densmap_dg_dyndomg_helix_d
>>   g_mindistg_order_dg_rms  g_sas_d  g_tcaf
>>  g_x2top_d grompp_dtpbconv_d
>> >> g_anadock g_chi_d  g_densorderg_dyndom_d
>> g_helixorient  g_mindist_d  g_pme_error  g_rms_dg_select
>>  g_tcaf_d g_xrama   make_editrjcat
>> >>
>> >>
>> >> Elsaid,
>> >>
>> >> Regarding Justin’s suggestion, on Uppmax I believe the full path would
>> be:
>> >>
>> >> source  /sw/apps/gromacs/4.6.3/tintin/bin/GMXRC.bash
>> >>
>> >>
>> >> However I think you already issued
>> >>
>> >> module load gromacs
>> >>
>> >> which might source GMXRC .
>> >>
&g

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