from:"Jefferies D . F ."

Re: [gmx-users] Umbrella sampling

2017-12-22 Thread Jefferies D . F .

All sorted now. 

Thanks, 

Damien 

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of 
sp...@iacs.res.in [sp...@iacs.res.in]
Sent: Friday, December 22, 2017 11:49 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Umbrella sampling

  - Message from Mark Abraham  -
Date: Fri, 22 Dec 2017 00:42:31 +
From: Mark Abraham 
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
  To: gmx-us...@gromacs.org
  Cc: gromacs.org_gmx-users@maillist.sys.kth.se

> Hi,
>
> Yes, the parsing of that file looks like it doesn't handle blank lines
> gracefully, at least. Use a text editor and clean things up. And make
sure
> the file endings are unix style, e.g. with dos2unix if relevant.
>
> Mark
>
> On Wed, Dec 20, 2017 at 7:57 AM Jefferies D.F. 
> wrote:
>
>> Out of curiosity, how did you manage to identify and subsequently remove
>> the extra space? I have been having similar problems and the tools I've
>> used haven't fixed this problem.
>>
>> Thanks,
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of
>> sp...@iacs.res.in [sp...@iacs.res.in]
>> Sent: Tuesday, December 19, 2017 6:21 PM
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: Re: [gmx-users] Umbrella sampling
>>
>>   - Message from Dhaniram Mahato  -
>> Date: Tue, 19 Dec 2017 21:30:05 +0800
>> From: Dhaniram Mahato 
>> Reply-To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Umbrella sampling
>>   To: gmx-us...@gromacs.org
>>
>> Hi,
>>
>> There could be format problem. You can create your own .dat files by
>> typing
>> it. You have probably copied it from somewhere. I hope it will work
then.
>>
>>
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html
>>
>> Thanks
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or send a mail to gmx-users-requ...@gromacs.org.
>>
>> Hii
>> I have solved the problem. It was just because of one extra space added
>> in
>> the tpr-files.dat file. Now its running properly.
>>
>> - End message from Dhaniram Mahato  -
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
>> --
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>
> --
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Thank you Mark for your suggestion.

- End message from Mark Abraham  -
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Re: [gmx-users] Umbrella sampling

2017-12-19 Thread Jefferies D . F .

Out of curiosity, how did you manage to identify and subsequently remove the 
extra space? I have been having similar problems and the tools I've used 
haven't fixed this problem.

Thanks,  

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of 
sp...@iacs.res.in [sp...@iacs.res.in]
Sent: Tuesday, December 19, 2017 6:21 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Umbrella sampling

  - Message from Dhaniram Mahato  -
Date: Tue, 19 Dec 2017 21:30:05 +0800
From: Dhaniram Mahato 
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
  To: gmx-us...@gromacs.org

> Hi,
>
> There could be format problem. You can create your own .dat files by
> typing
> it. You have probably copied it from somewhere. I hope it will work then.
>
>
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html
>
> Thanks
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests
> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or send a mail to gmx-users-requ...@gromacs.org.

Hii
I have solved the problem. It was just because of one extra space added in
the tpr-files.dat file. Now its running properly.

- End message from Dhaniram Mahato  -
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Re: [gmx-users] Problem using gmx wham

2017-11-14 Thread Jefferies D . F .

Hi Justin, 

Thanks for your response. I've attempted to run gmx wham using GROMACS 5.1.4 
and I seem to get the same problem, even if I attempt to use dos2unix before I 
issue a command i.e.
---
Program gmx wham, VERSION 5.1.4
Source code file: 
/local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp,
 line: 1800

Fatal error:
Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.

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

I've taken a look at older posts relating to this problem, and I saw that a 
similar complaint was resolved after the poster used dos2unix (following your 
recommendation). But that hasn't seemed to work for me. 

Regards,

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: Tuesday, November 14, 2017 2:35 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem using gmx wham

At least upgrade to the latest release in the series (5.1.4) or better
yet, the actual latest version (2016.4) to see if this is a bug that's
been fixed. I seem to recall this same behavior reported before and
subsequently solved, but haven't dug it up.

-Justin

On 11/13/17 7:11 AM, Jefferies D.F. wrote:
> Hey guys,
>
> Sorry if it seems that I'm bumping this thread, but I was wondering if anyone 
> had any other suggestions before I let this thread die.
>
> Thanks.
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Jefferies 
> D.F. [dfj1...@soton.ac.uk]
> Sent: Thursday, November 02, 2017 1:29 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Problem using gmx wham
>
> Hi Justin,
>
> Thanks for the response. The .dat files were created with the vi text editor, 
> they contain lists of the .tpr and .xvg to be read, e.g.
>
> umbrella0.tpr
> umbrella1.tpr
> umbrella2.tpr
> ..
> umbrella52.tpr
>
> I've tried to use dos2unix,  i.e.
> ~> dos2unix tpr-files.dat
> and
> ~> dos2unix pullf-files.dat
>
> but I still get the same error message i.e.
>
> ---
> Program gmx wham, VERSION 5.1.2
> Source code file: 
> /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 
> 1800
>
> Fatal error:
> Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> That being said, it seems you're correct in thinking something's weird with 
> the input files. After I created new .dat files, I got this message:
>
> ---
> Program gmx wham, VERSION 5.1.2
> Source code file: 
> /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 
> 3610
>
> Fatal error:
> Found 53 file names in tpr-files.dat, but 54 in pullf-files.dat
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> gmx wham is registering 54 files, when only 53 were written.
>
>
>
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin 
> Lemkul [jalem...@vt.edu]
> Sent: Thursday, November 02, 2017 11:10 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Problem using gmx wham
>
> On 11/1/17 4:26 PM, Jefferies D.F. wrote:
>> Hi,
>>
>> I am attempting to use gmx wham to compute a potential of mean force. I have 
>> used the command line:
>>
>> gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ
>>
>> where tpr-files.dat and pullf-files.dat contain a list of the .tpr and 
>> pullf.xvg files from each umbrella sampling window, respectively.
>>
>> It seems that gmx wham is having trouble reading the .tpr and .xvg files, as 
>> I get this error message:
>>
>> ---
>>
>> Program gmx wham, VERSION 5.1.4
>>
>> Source code file: 
>> /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp,
>>  line: 1800
>>
>>
>> Fatal error:
>>
>> Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.
>>
> The extra space after "tpr" in the printed error suggests something is
> weird with the input .dat file. Did you create it with a proper plain
> text editor? What about running dos2unix on it to make sure you've got
> the right kind of line endings?
>
> -Justin
>
>> For more

Re: [gmx-users] Problem using gmx wham

2017-11-13 Thread Jefferies D . F .

Hey guys,

Sorry if it seems that I'm bumping this thread, but I was wondering if anyone 
had any other suggestions before I let this thread die. 

Thanks.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Jefferies D.F. 
[dfj1...@soton.ac.uk]
Sent: Thursday, November 02, 2017 1:29 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem using gmx wham

Hi Justin,

Thanks for the response. The .dat files were created with the vi text editor, 
they contain lists of the .tpr and .xvg to be read, e.g.

umbrella0.tpr
umbrella1.tpr
umbrella2.tpr
..
umbrella52.tpr

I've tried to use dos2unix,  i.e.
~> dos2unix tpr-files.dat
and
~> dos2unix pullf-files.dat

but I still get the same error message i.e.

---
Program gmx wham, VERSION 5.1.2
Source code file: 
/Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 
1800

Fatal error:
Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.

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

That being said, it seems you're correct in thinking something's weird with the 
input files. After I created new .dat files, I got this message:

---
Program gmx wham, VERSION 5.1.2
Source code file: 
/Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 
3610

Fatal error:
Found 53 file names in tpr-files.dat, but 54 in pullf-files.dat

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

gmx wham is registering 54 files, when only 53 were written.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: Thursday, November 02, 2017 11:10 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem using gmx wham

On 11/1/17 4:26 PM, Jefferies D.F. wrote:
> Hi,
>
> I am attempting to use gmx wham to compute a potential of mean force. I have 
> used the command line:
>
> gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ
>
> where tpr-files.dat and pullf-files.dat contain a list of the .tpr and 
> pullf.xvg files from each umbrella sampling window, respectively.
>
> It seems that gmx wham is having trouble reading the .tpr and .xvg files, as 
> I get this error message:
>
> ---
>
> Program gmx wham, VERSION 5.1.4
>
> Source code file: 
> /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp,
>  line: 1800
>
>
> Fatal error:
>
> Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.
>

The extra space after "tpr" in the printed error suggests something is
weird with the input .dat file. Did you create it with a proper plain
text editor? What about running dos2unix on it to make sure you've got
the right kind of line endings?

-Justin

> For more information and tips for troubleshooting, please check the GROMACS
>
> website at http://www.gromacs.org/Documentation/Errors
>
> ---
>
>
> I have computed potential of mean force profiles before (using this Mac), but 
> I haven't encountered this problem. Could someone help me with this problem?
>
>

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] Problem using gmx wham

2017-11-02 Thread Jefferies D . F .

Hi Justin, 

Thanks for the response. The .dat files were created with the vi text editor, 
they contain lists of the .tpr and .xvg to be read, e.g.

umbrella0.tpr
umbrella1.tpr
umbrella2.tpr
..
umbrella52.tpr 

I've tried to use dos2unix,  i.e. 
~> dos2unix tpr-files.dat
and 
~> dos2unix pullf-files.dat

but I still get the same error message i.e. 

---
Program gmx wham, VERSION 5.1.2
Source code file: 
/Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 
1800

Fatal error:
Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.

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

That being said, it seems you're correct in thinking something's weird with the 
input files. After I created new .dat files, I got this message:

---
Program gmx wham, VERSION 5.1.2
Source code file: 
/Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 
3610

Fatal error:
Found 53 file names in tpr-files.dat, but 54 in pullf-files.dat

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

gmx wham is registering 54 files, when only 53 were written.  

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: Thursday, November 02, 2017 11:10 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem using gmx wham

On 11/1/17 4:26 PM, Jefferies D.F. wrote:
> Hi,
>
> I am attempting to use gmx wham to compute a potential of mean force. I have 
> used the command line:
>
> gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ
>
> where tpr-files.dat and pullf-files.dat contain a list of the .tpr and 
> pullf.xvg files from each umbrella sampling window, respectively.
>
> It seems that gmx wham is having trouble reading the .tpr and .xvg files, as 
> I get this error message:
>
> ---
>
> Program gmx wham, VERSION 5.1.4
>
> Source code file: 
> /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp,
>  line: 1800
>
>
> Fatal error:
>
> Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.
>

The extra space after "tpr" in the printed error suggests something is
weird with the input .dat file. Did you create it with a proper plain
text editor? What about running dos2unix on it to make sure you've got
the right kind of line endings?

-Justin

> For more information and tips for troubleshooting, please check the GROMACS
>
> website at http://www.gromacs.org/Documentation/Errors
>
> ---
>
>
> I have computed potential of mean force profiles before (using this Mac), but 
> I haven't encountered this problem. Could someone help me with this problem?
>
>

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] Problem using gmx wham

2017-11-01 Thread Jefferies D . F .

Hi,

I am attempting to use gmx wham to compute a potential of mean force. I have 
used the command line:

gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ

where tpr-files.dat and pullf-files.dat contain a list of the .tpr and 
pullf.xvg files from each umbrella sampling window, respectively.

It seems that gmx wham is having trouble reading the .tpr and .xvg files, as I 
get this error message:

---

Program gmx wham, VERSION 5.1.4

Source code file: 
/local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp,
 line: 1800


Fatal error:

Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.


For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

---


I have computed potential of mean force profiles before (using this Mac), but I 
haven't encountered this problem. Could someone help me with this problem?


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Re: [gmx-users] Umbrella sampling

Re: [gmx-users] Umbrella sampling

Re: [gmx-users] Problem using gmx wham

Re: [gmx-users] Problem using gmx wham

Re: [gmx-users] Problem using gmx wham

[gmx-users] Problem using gmx wham

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