Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

[Groenhof, Gerrit]

Hi,

Does it run with the cutoff-scheme=group? 

Gerrit





After trying a few different settings of .mdp, I found that "cutoff-scheme = 
Verlet" and "QMMMscheme = ONIOM" were causing the error.  Would you have any 
idea how were these two settings linked to the generation of ".pc" file, and 
what would you suggest if I have to run under ONIOM?


Thank you.


Best regards,

Zoe



From: CHAN, Zoe ZC [Student] 
Sent: 27 November 2017 18:23
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

Dear Gerrit,

Thank you very much for your prompt reply.
I?ve tried to run the simulation with wenjin?s tutorial and it passed the point 
charge correction step with no problem. I compared the ?.out? output files of 
my protein and of the tutorial peptide, I noticed there?s a line ?%pointcharges 
?peptide.pc?? at the end of the input file section, I guess it shows that the 
basename has been linked to the ?.pc? point charge file instead of the default 
name ?temp.pc?, and it?s missing in my protein?s output file. Would that have 
possibly caused the crash?
Again, thank you for your help.

Best regards,
Zoe

On 27 Nov 2017, at 6:11 PM, Groenhof, Gerrit 
> wrote:

>From the error message it seems that ORCA program crashes. Unfortunately, Orca 
>is no longer supported, which means that if the ORCA's input or anything else 
>has changed, the gromacs interface may fail.

What you could try is to use the version of ORCA that others have used before.

Best,

Gerrit





Content-Type: text/plain; charset="iso-8859-1"

Dear Gromacs Users,


I've been running a QM/MM calculation on a protein with fluorescence probe, 
using gromacs 4.6.7 (double precision with MPI) and ORCA 4.0.1.  The following 
lines were included in the .mdp file,


QMMM = yes
QMMM-grps= QMatoms
QMmethod  = B3LYP
QMbasis  = 6-31G*
QMMMscheme   = ONIOM
QMcharge   = -2
QMmult= 2

The run was aborted with the error messages,


FATAL ERROR ENCOUNTERED
CANNOT OPEN FILE
Filename: temp.pc

*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: (nil)
[ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x2ba5c5ada390]
[ 1] /lib/x86_64-linux-gnu/libc.so.6(fgets+0x1e)[0x2ba5c5d53aee]
[ 2] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(read_orca_output+0x1d8)[0x2ba5c4959b98]
[ 3] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(call_orca+0xf0)[0x2ba5c495a0d0]
[ 4] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(calculate_QMMM+0xa67)[0x2ba5c496a647]
[ 5] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force_lowlevel+0x1629)[0x2ba5c487cdf9]
[ 6] 
/usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force_cutsVERLET+0x17bb)[0x2ba5c48cc31b]
[ 7] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force+0x17f)[0x2ba5c48d02ef]
[ 8] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_steep+0x5b3)[0x2ba5c48e4c33]
[ 9] mdrun_mpi_d(mdrunner+0x15f2)[0x40f172]
[10] mdrun_mpi_d(cmain+0x1a17)[0x433f67]
[11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x2ba5c5d06830]
[12] mdrun_mpi_d(_start+0x29)[0x4072b9]
*** End of error message ***
Segmentation fault (core dumped)


I am clueless on where the error came from, would anyone have any insight?  
Thank you.


Best regards,

Zoe

[http://mlm.polyu.edu.hk/PolyU80_Email_Signature.png]

www.polyu.edu.hk/80anniversary

Disclaimer:

This message (including any attachments) contains confidential information 
intended for a specific individual and purpose. If you are not the intended 
recipient, you should delete this message and notify the sender and The Hong 
Kong Polytechnic University (the University) immediately. Any disclosure, 
copying, or distribution of this message, or the taking of any action based on 
it, is strictly prohibited and may be unlawful.

The University specifically denies any responsibility for the accuracy or 
quality of information obtained through University E-mail Facilities. Any views 
and opinions expressed are only those of the author(s) and do not necessarily 
represent those of the University and the University accepts no liability 
whatsoever for any losses or damages incurred or caused to any party as a 
result of the use of such information.


--

--
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Distances calculation in umbrella sampling

[Amir Zeb]

Hello gmx users,

I want to calculate binding free energy for protein-ligand complex by
Umbrella sampling in Gromacs. I have extracted each frame's gro file for
500 frames after pulling simulation. Now, I want to calculate the distances
between the representative gro files by executing the script given by Dr.
Justin in his tutorial. I have replaced the Chain_A by ligand name and
Chain_B by Protein_ZN in original script to represent my index file groups.
The summary_distances.dat file is generating successfully, but it has no
distances information. Only frames number are given on a single column and
is repeated again after 500th frame. The summary_distances.dat file is
attached for your kind consideration.
Please let me know if there is any possibility to fix this issue.

Thanks in advance!
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] water molecule cannot be settled

[MD]

Ok, thank you Justin.
Ming

On Nov 29, 2017 6:55 PM, "Justin Lemkul"  wrote:

>
>
> On 11/29/17 6:53 PM, MD wrote:
>
>> Hi Justin,
>> Can you tell me where you spotted the broken topology? And where should I
>> get in to get it fixed?
>>
>
> "System has non-zero total charge: -0.859995"
>
> Can any molecule have a fraction of an electron?
>
> Whatever you've manually parametrized is incorrect.
>
> -Justin
>
> Thanks,
>> Ming
>>
>> On Nov 29, 2017 6:15 PM, "Justin Lemkul"  wrote:
>>
>>
>>> On 11/29/17 3:26 PM, MD wrote:
>>>
>>> Hi,

 I was trying to minimize a solvated structure with following commands
 but
 I
 got stuck at an error message complaining about water molecule not
 settled
 when I was trying to 'gmx mdrun -v -deffnm em'.  I copied the grompp and
 mdrun command, log file and the error message after the command. Any
 help
 will be appreciated.

 'gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr'

 NOTE 1 [file em_real.mdp]:
 With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20.
 Note
 that with the Verlet scheme, nstlist has no effect on the accuracy
 of
 your simulation.

 Setting the LD random seed to 2057414563
 Generated 97877 of the 97903 non-bonded parameter combinations
 Generating 1-4 interactions: fudge = 1
 Generated 64492 of the 97903 1-4 parameter combinations
 Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
 Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
 Excluding 3 bonded neighbours molecule type 'Other_chain_B'
 Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
 Excluding 2 bonded neighbours molecule type 'SOL'
 Excluding 1 bonded neighbours molecule type 'NA'

 NOTE 2 [file topol.top, line 53]:
 System has non-zero total charge: -0.859995
 Total charge should normally be an integer. See
 http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
 for discussion on how close it should be to an integer.


 You have a fundamentally broken topology. Don't attempt any simulation
>>> with such a topology until you correct it.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] water molecule cannot be settled

[Justin Lemkul]

On 11/29/17 6:53 PM, MD wrote:

Hi Justin,
Can you tell me where you spotted the broken topology? And where should I
get in to get it fixed?


"System has non-zero total charge: -0.859995"

Can any molecule have a fraction of an electron?

Whatever you've manually parametrized is incorrect.

-Justin


Thanks,
Ming

On Nov 29, 2017 6:15 PM, "Justin Lemkul"  wrote:



On 11/29/17 3:26 PM, MD wrote:


Hi,

I was trying to minimize a solvated structure with following commands but
I
got stuck at an error message complaining about water molecule not settled
when I was trying to 'gmx mdrun -v -deffnm em'.  I copied the grompp and
mdrun command, log file and the error message after the command. Any help
will be appreciated.

'gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr'

NOTE 1 [file em_real.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.

Setting the LD random seed to 2057414563
Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
Excluding 3 bonded neighbours molecule type 'Other_chain_B'
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'

NOTE 2 [file topol.top, line 53]:
System has non-zero total charge: -0.859995
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.



You have a fundamentally broken topology. Don't attempt any simulation
with such a topology until you correct it.

-Justin

--
==

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

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

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

==

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.



--
==

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

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

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

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] water molecule cannot be settled

[MD]

Hi Justin,
Can you tell me where you spotted the broken topology? And where should I
get in to get it fixed?
Thanks,
Ming

On Nov 29, 2017 6:15 PM, "Justin Lemkul"  wrote:

>
>
> On 11/29/17 3:26 PM, MD wrote:
>
>> Hi,
>>
>> I was trying to minimize a solvated structure with following commands but
>> I
>> got stuck at an error message complaining about water molecule not settled
>> when I was trying to 'gmx mdrun -v -deffnm em'.  I copied the grompp and
>> mdrun command, log file and the error message after the command. Any help
>> will be appreciated.
>>
>> 'gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr'
>>
>> NOTE 1 [file em_real.mdp]:
>>With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>>that with the Verlet scheme, nstlist has no effect on the accuracy of
>>your simulation.
>>
>> Setting the LD random seed to 2057414563
>> Generated 97877 of the 97903 non-bonded parameter combinations
>> Generating 1-4 interactions: fudge = 1
>> Generated 64492 of the 97903 1-4 parameter combinations
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
>> Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
>> Excluding 3 bonded neighbours molecule type 'Other_chain_B'
>> Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
>> Excluding 2 bonded neighbours molecule type 'SOL'
>> Excluding 1 bonded neighbours molecule type 'NA'
>>
>> NOTE 2 [file topol.top, line 53]:
>>System has non-zero total charge: -0.859995
>>Total charge should normally be an integer. See
>>http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>>for discussion on how close it should be to an integer.
>>
>>
> You have a fundamentally broken topology. Don't attempt any simulation
> with such a topology until you correct it.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] There is no domain decomposition for n nodes that is compatible with the given box and a minimum cell size of x nm

[Justin Lemkul]

On 11/29/17 5:43 PM, MD wrote:

Hi folks,

I got a fatal error when running em.mdp. Do you think if it is the .mdp
that is causing this issue?


My command line is : gmx mdrun -v -deffnm em

The Fatal error:
"There is no domain decomposition for 40 ranks that is compatible with the
given box and a minimum cell size of 2.42098 nm. Change the number of ranks
or mdrun option -rdd"


Try Google. This error has been asked and answered a hundred times over.

-Justin

--
==

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

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

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

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] mdrun (nvt.mdp) wouldn't work

[Justin Lemkul]

On 11/29/17 5:02 PM, MD wrote:

Hi gromacs folks,

I was trying to do a mdrun using nvt.mdp and I got following error
messages. I am not quite sure what is causing the error and I am hoping to
get some help here. Is it because my starting structure is not good enough?
There were some broken residues but I had them fixed and the minimization
run was ok until the equilibration.

The command and notes  I had was as followed.


*  gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr*

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12#
Setting the LD random seed to 552293178
Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Other_chain_B'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...

NOTE 1 [file topol.top, line 53]:
   System has non-zero total charge: 0.140005
   Total charge should normally be an integer. See
   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
   for discussion on how close it should be to an integer.


This is the same error as your previous question. Don't ignore grompp 
when it's trying to help you avoid really bad mistakes.


-Justin

--
==

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

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

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

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] water molecule cannot be settled

[Justin Lemkul]

On 11/29/17 3:26 PM, MD wrote:

Hi,

I was trying to minimize a solvated structure with following commands but I
got stuck at an error message complaining about water molecule not settled
when I was trying to 'gmx mdrun -v -deffnm em'.  I copied the grompp and
mdrun command, log file and the error message after the command. Any help
will be appreciated.

'gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr'

NOTE 1 [file em_real.mdp]:
   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
   that with the Verlet scheme, nstlist has no effect on the accuracy of
   your simulation.

Setting the LD random seed to 2057414563
Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
Excluding 3 bonded neighbours molecule type 'Other_chain_B'
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'

NOTE 2 [file topol.top, line 53]:
   System has non-zero total charge: -0.859995
   Total charge should normally be an integer. See
   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
   for discussion on how close it should be to an integer.



You have a fundamentally broken topology. Don't attempt any simulation 
with such a topology until you correct it.


-Justin

--
==

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

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

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

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 11/29/17 2:45 PM, rose rahmani wrote:

Hello;

would you please send me Mr.lemkul's article link ? i can't find them.


It's linked here: 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/01_pdb2gmx.html


If you need something regarding my published research, contact me 
directly. This really has nothing to do with GROMACS.


-Justin

--
==

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

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

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

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] gmx distance,umbrella sampling

[Justin Lemkul]

On 11/29/17 11:02 AM, rose rahmani wrote:

Hello;

would you please tell me how gmx distance calculate and write COM distance
from .gro and .tpr files excactly?


No one can give you an "exact" command because selections will depend on 
what you want to do, but in general, the syntax is here:


http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0#g_dist

-Justin

--
==

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

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

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

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] There is no domain decomposition for n nodes that is compatible with the given box and a minimum cell size of x nm

[MD]

Hi folks,

I got a fatal error when running em.mdp. Do you think if it is the .mdp
that is causing this issue?


My command line is : gmx mdrun -v -deffnm em

The Fatal error:
"There is no domain decomposition for 40 ranks that is compatible with the
given box and a minimum cell size of 2.42098 nm. Change the number of ranks
or mdrun option -rdd"


em.log is as followed.

Input Parameters:
   integrator = steep
   tinit  = 0
   dt = 0.001
   nsteps = 5
   init-step  = 0
   simulation-part= 1
   comm-mode  = Linear
   nstcomm= 100
   bd-fric= 0
   ld-seed= -563054091
   emtol  = 1000
   emstep = 0.01
   niter  = 20
   fcstep = 0
   nstcgsteep = 1000
   nbfgscorr  = 10
   rtpi   = 0.05
   nstxout= 0
   nstvout= 0
   nstfout= 0
   nstlog = 1000
   nstcalcenergy  = 100
   nstenergy  = 1000
   nstxout-compressed = 0
   compressed-x-precision = 1000
   cutoff-scheme  = Verlet
   nstlist= 1
   ns-type= Grid
   pbc= xyz
   periodic-molecules = false
   verlet-buffer-tolerance= 0.005
   rlist  = 1
   coulombtype= PME
   coulomb-modifier   = Potential-shift
   rcoulomb-switch= 0
   rcoulomb   = 1
   epsilon-r  = 1
   epsilon-rf = inf
   vdw-type   = Cut-off
   vdw-modifier   = Potential-shift
   rvdw-switch= 0
   rvdw   = 1
   DispCorr   = No
   table-extension= 1
   fourierspacing = 0.12
   fourier-nx = 96
   fourier-ny = 96
   fourier-nz = 96
   pme-order  = 4
   ewald-rtol = 1e-05
   ewald-rtol-lj  = 0.001
   lj-pme-comb-rule   = Geometric
   ewald-geometry = 0
   epsilon-surface= 0
   implicit-solvent   = No
   gb-algorithm   = Still
   nstgbradii = 1
   rgbradii   = 1
   gb-epsilon-solvent = 80
   gb-saltconc= 0
   gb-obc-alpha   = 1
   gb-obc-beta= 0.8
   gb-obc-gamma   = 4.85
   gb-dielectric-offset   = 0.009
   sa-algorithm   = Ace-approximation
   sa-surface-tension = 2.05016
   tcoupl = No
   nsttcouple = -1
   nh-chain-length= 0
   print-nose-hoover-chain-variables = false
   pcoupl = No
   pcoupltype = Isotropic
   nstpcouple = -1
   tau-p  = 1
   compressibility (3x3):
  compressibility[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compressibility[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compressibility[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   ref-p (3x3):
  ref-p[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref-p[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref-p[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   refcoord-scaling   = No
   posres-com (3):
  posres-com[0]= 0.0e+00
  posres-com[1]= 0.0e+00
  posres-com[2]= 0.0e+00
   posres-comB (3):
  posres-comB[0]= 0.0e+00
  posres-comB[1]= 0.0e+00
  posres-comB[2]= 0.0e+00
   QMMM   = false
   QMconstraints  = 0
   QMMMscheme = 0
   MMChargeScaleFactor= 1
qm-opts:
   ngQM   = 0
   constraint-algorithm   = Lincs
   continuation   = false
   Shake-SOR  = false
   shake-tol  = 0.0001
   lincs-order= 4
   lincs-iter = 1
   lincs-warnangle= 30
   nwall  = 0
   wall-type  = 9-3
   wall-r-linpot  = -1
   wall-atomtype[0]   = -1
   wall-atomtype[1]   = -1
   wall-density[0]= 0
   wall-density[1]= 0
   wall-ewald-zfac= 3
   pull   = false
   rotation   = false
   

[gmx-users] mdrun (nvt.mdp) wouldn't work

[MD]

Hi gromacs folks,

I was trying to do a mdrun using nvt.mdp and I got following error
messages. I am not quite sure what is causing the error and I am hoping to
get some help here. Is it because my starting structure is not good enough?
There were some broken residues but I had them fixed and the minimization
run was ok until the equilibration.

The command and notes  I had was as followed.


*  gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr*

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12#
Setting the LD random seed to 552293178
Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Other_chain_B'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...

NOTE 1 [file topol.top, line 53]:
  System has non-zero total charge: 0.140005
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.



Setting gen_seed to 2333002834
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet
Number of degrees of freedom in T-Coupling group Protein_MG_ATP is 11217.68
Number of degrees of freedom in T-Coupling group NA_SOL is 94242.32
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.432 nm, buffer size 0.032 nm
Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 60x60x60, spacing 0.152 0.152 0.152
Estimate for the relative computational load of the PME mesh part: 0.08
This run will generate roughly 126 Mb of data

There was 1 note

Back Off! I just backed up nvt.tpr to ./#nvt.tpr.1#

gcq#207: "Is That a Real Poncho ?" (F. Zappa)



*gmx mdrun -deffnm nvt*


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004922, max 0.143141 (between atoms 4646 and 4648)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
starting mdrun 'Protein in water'
5 steps,100.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.018958, max 0.925037 (between atoms 4628 and 4630)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4608   4609   32.00.1016   0.1180  0.0997
   4608   4610   33.70.1555   0.2089  0.1430
  ...
Wrote pdb files with previous and current coordinates

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.015813, max 0.806353 (between atoms 4630 and 4631)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4608   4609   30.40.1180   0.1065  0.0997
   4608   4610   39.20.2089   0.1668  0.1430
  ...
Wrote pdb files with previous and current coordinates

Step 2, time 0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.020826, max 0.666994 (between atoms 4628 and 4630)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4598   4606   42.20.1770   0.1820  0.1490
   4606   4607   48.70.1290   0.1290  0.1230
   ...
Wrote pdb files with previous and current coordinates

Step 3, time 0.006 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 3.113067, max 231.822983 (between atoms 4610 and 4611)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4570   4571   42.80.1273   0.1912  0.1230
   4572   4573   87.40.1000   0.0886  0.0997
   4572   4574   54.90.1738   0.2588  0.1430
   ...
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 4606 and 4611
at distance 25.173 which is larger than the table limit 2.431 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several 

[gmx-users] water molecule cannot be settled

[MD]

Hi,

I was trying to minimize a solvated structure with following commands but I
got stuck at an error message complaining about water molecule not settled
when I was trying to 'gmx mdrun -v -deffnm em'.  I copied the grompp and
mdrun command, log file and the error message after the command. Any help
will be appreciated.

'gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr'

NOTE 1 [file em_real.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 2057414563
Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
Excluding 3 bonded neighbours molecule type 'Other_chain_B'
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'

NOTE 2 [file topol.top, line 53]:
  System has non-zero total charge: -0.859995
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.



Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:   345Protein residues
There are:14Ion residues
There are: 1  Other residues
There are: 18022  Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group rest is 125097.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 80x80x80, spacing 0.119 0.119 0.119
Estimate for the relative computational load of the PME mesh part: 0.20
This run will generate roughly 5 Mb of data

There were 2 notes


'gmx mdrun -v -deffnm em'

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

WARNING: Listed nonbonded interaction between particles 4630 and 4646
at distance 2.141 which is larger than the table limit 2.000 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.


Step=0, Dmax= 1.0e-02 nm, Epot=  1.37831e+08 Fmax= 2.33474e+10, atom=
5382
Step=1, Dmax= 1.0e-02 nm, Epot=  8.10627e+06 Fmax= 9.06678e+08, atom=
5382
Step=2, Dmax= 1.2e-02 nm, Epot=  1.57170e+06 Fmax= 5.63829e+07, atom=
5383
Step=3, Dmax= 1.4e-02 nm, Epot=  4.98801e+05 Fmax= 1.15297e+07, atom=
5381
Step=4, Dmax= 1.7e-02 nm, Epot=  2.84347e+05 Fmax= 2.00959e+06, atom=
5381
Step=5, Dmax= 2.1e-02 nm, Epot=  1.73937e+05 Fmax= 5.63524e+05, atom=
4644
Step=6, Dmax= 2.5e-02 nm, Epot=  8.01156e+04 Fmax= 5.40120e+05, atom=
4644
Step=7, Dmax= 3.0e-02 nm, Epot=  1.58428e+04 Fmax= 5.15983e+05, atom=
4644
Step=8, Dmax= 3.6e-02 nm, Epot= -4.53540e+04 Fmax= 4.90339e+05, atom=
4644
Step=9, Dmax= 4.3e-02 nm, Epot= -1.02816e+05 Fmax= 4.58354e+05, atom=
4644
Step=   10, Dmax= 5.2e-02 nm, Epot= -1.54031e+05 Fmax= 4.23043e+05, atom=
4644
Step=   11, Dmax= 6.2e-02 nm, Epot= -2.10519e+05 Fmax= 1.10326e+06, atom=
4651
Step=   12, Dmax= 7.4e-02 nm, Epot= -2.22123e+05 Fmax= 3.74510e+05, atom=
4646
Step=   13, Dmax= 8.9e-02 nm, Epot= -2.99577e+05 Fmax= 2.76027e+05, atom=
4646
Step=   14, Dmax= 1.1e-01 nm, Epot= -3.65363e+05 Fmax= 6.32069e+05, atom=
4651
Step=   16, Dmax= 6.4e-02 nm, Epot= -3.79471e+05 Fmax= 1.98011e+05, atom=
4646
Step=   17, Dmax= 7.7e-02 nm, Epot= -4.21782e+05 Fmax= 1.09246e+05, atom=
4647
Step=   18, Dmax= 9.2e-02 nm, Epot= -4.79158e+05 Fmax= 1.69343e+05, atom=
4646
Step=   19, Dmax= 1.1e-01 nm, Epot= -4.92508e+05 Fmax= 3.68756e+05, atom=
4646

Back Off! I just backed up step20b.pdb to ./#step20b.pdb.1#

Back Off! I just backed up step20c.pdb to ./#step20c.pdb.1#
Wrote pdb files with previous and current coordinates



[em.mdp]

integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0  ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps = 5   ; Maximum number of (minimization) steps to perform
energygrps = Protein ; Which energy group(s) to write to disk

; Parameters describing how to find the 

Re: [gmx-users] question of perturbing order in single topology FEP, gromacs

[Peng He]

Hi, Asaf,

Thank you very much for your suggestions, I am not sure I understand it
correctly.

2017-11-29 13:22 GMT-05:00 :

> Dear Peng,
>
> You can transform each of the molecules seperately.

You can remove the nonbonded interactions of the atoms that are different
> between the compared molecules.
>
Does it mean when going from A-B to A-C, decouple the B's nonbonded than
coupling the C's nonbonded interaction?

> Then, if you have only one dihedral relating the different atoms to the
> common atoms in each molecule it does not need to be removed. Also, the
> bond angle and covalent bond terms do not need to be removed. This is based
> on NVT but may be also accurate for NPT.
>
In the Ethane -> methanol case, the C-C bond length decreases from 1.5 to
1.4 when perturbing to C-O bond, and the kappa for the bond also changes, I
am not sure but I think we can use bonded lambdas to perturb the bond, I
did not remove any bond or angle in this case.
I think what you suggest is dual topology method which contains a dummy CH3
group in Methanol and a dummy OH group in Ethane, in that case I don't need
to change the bond length and angle, and it would not create such different
free energy values. I really test it in dual topology method and there is
little effect from the order of perturbations.
>
> We also saw that the order of transforming matters but maybe you can try
> without removing the bonded terms.


> For more details you can read:
> http://www.sciencedirect.com/science/article/pii/S0010465516303411
>
> Best,
> Asaf
>
>
> Quoting Peng He :
>
> HI, all,
>>
>> I am recently doing some test FEP calculations to get familiar, I am
>> preparing a system of ethane -> methanol using Amber gaff force field and
>> single topology method.
>>
>> "  4 [ atomtypes ]
>>   5 ;name   bond_type mass charge   ptype   sigma epsilon
>> Amb
>>   6  c3   c3  0.0  0.0   A 3.39967e-01
>> 4.57730e-01 ; 1.91  0.1094
>>   7  hc   hc  0.0  0.0   A 2.64953e-01
>> 6.56888e-02 ; 1.49  0.0157
>>   8  oh   oh  0.0  0.0   A 3.06647e-01
>> 8.80314e-01 ; 1.72  0.2104
>>   9  h1   h1  0.0  0.0   A 2.47135e-01
>> 6.56888e-02 ; 1.39  0.0157
>>  10  dh   hc  0.0  0.0   A 0.0  0.0
>>  11  ho   ho  0.0  0.0   A 0.0e+00
>>  0.0e+00
>>  12 [ moleculetype ]
>>  13 ;namenrexcl
>>  14  UNK  3
>>  15
>>  16 [ atoms ]
>>  17 ;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
>> bond_type
>>  18  1   c3 1   UNKC11-0.095100 12.01000   c3
>>  0.11670012.01000
>>  19  2   c3 1   UNKC22-0.095100 12.01000   oh
>> -0.59880112.01000
>>  20  3   hc 1   UNKH13 0.031700  1.00800   h1
>>  0.028700 1.00800
>>  21  4   hc 1   UNKH24 0.031700  1.00800   h1
>>  0.028700 1.00800
>>  22  5   hc 1   UNKH35 0.031700  1.00800   h1
>>  0.028700 1.00800
>>  23  6   hc 1   UNKH46 0.031700  1.00800   ho
>>  0.396000 1.00800
>>  24  7   hc 1   UNKH57 0.031700  1.00800   dh
>>  0.00 1.00800
>>  25  8   hc 1   UNKH68 0.031700  1.00800   dh
>>  0.00 1.00800
>>  26
>>  27 [ bonds ]
>>  28 ;   ai aj funct   r k
>>  29  1  2   11.5375e-012.5179e+05  1.4233e-01
>> 2.6501e+05
>>  30  1  3   11.0969e-012.7665e+05  1.0969e-01
>> 2.7665e+05
>>  31  1  4   11.0969e-012.7665e+05  1.0969e-01
>> 2.7665e+05
>>  32  1  5   11.0969e-012.7665e+05  1.0969e-01
>> 2.7665e+05
>>  33  2  6   11.0969e-012.7665e+05  9.7300e-02
>> 3.1079e+05
>>  34  2  7   11.0969e-012.7665e+05  1.0969e-01
>> 2.7665e+05
>>  35  2  8   11.0969e-012.7665e+05  1.0969e-01
>> 2.7665e+05
>> ...
>> ..."
>>
>> I know to perturbing from large molecule(ethane) to small(methanol), I
>> need
>> to perturb the electrostatic interaction first than vdw, But I don't know
>> where to perturb the bonded lambdas. I have tested different orders of
>> Bonded lambdas, and I have got a quite different answer which seems odd to
>> me. I have a table for that
>> stage1 stage2 stage3 dG(kj) dG(kcal)
>> single topology solv q/bonded/vdw -14.36 -3.43
>> bonded q vdw -13.79 -3.30
>> bonded/q vdw -14.91 -3.56
>> q bonded vdw -17.13 -4.09
>> q bonded/vdw -20.22 -4.83
>> q vdw bonded -25.2 -6.02
>> single topology vac q/bonded/vdw 10.32 2.47
>> bonded q vdw 9.53 2.28
>> bonded/q vdw 9.1 2.17
>> q bonded vdw 8.71 2.08
>> q bonded/vdw 9.64 2.30
>> q vdw bonded 9.84 2.35
>> The desolvation free energy of ethane is -2.48 and methanol 3.48kcal.
>> The best result which close the cyclo for ethane,vac -> ethane, solv ->
>> methanol, solv 

[gmx-users] umbrella sampling

[rose rahmani]

Hello;

would you please send me Mr.lemkul's article link ? i can't find them.

Thank you
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] question of perturbing order in single topology FEP, gromacs

[asaffarhi]

Dear Peng,

You can transform each of the molecules seperately.
You can remove the nonbonded interactions of the atoms that are  
different between the compared molecules.
Then, if you have only one dihedral relating the different atoms to  
the common atoms in each molecule it does not need to be removed.  
Also, the bond angle and covalent bond terms do not need to be  
removed. This is based on NVT but may be also accurate for NPT.
We also saw that the order of transforming matters but maybe you can  
try without removing the bonded terms.


For more details you can read:
http://www.sciencedirect.com/science/article/pii/S0010465516303411

Best,
Asaf


Quoting Peng He :


HI, all,

I am recently doing some test FEP calculations to get familiar, I am
preparing a system of ethane -> methanol using Amber gaff force field and
single topology method.

"  4 [ atomtypes ]
  5 ;name   bond_type mass charge   ptype   sigma epsilon
Amb
  6  c3   c3  0.0  0.0   A 3.39967e-01
4.57730e-01 ; 1.91  0.1094
  7  hc   hc  0.0  0.0   A 2.64953e-01
6.56888e-02 ; 1.49  0.0157
  8  oh   oh  0.0  0.0   A 3.06647e-01
8.80314e-01 ; 1.72  0.2104
  9  h1   h1  0.0  0.0   A 2.47135e-01
6.56888e-02 ; 1.39  0.0157
 10  dh   hc  0.0  0.0   A 0.0  0.0
 11  ho   ho  0.0  0.0   A 0.0e+00   0.0e+00
 12 [ moleculetype ]
 13 ;namenrexcl
 14  UNK  3
 15
 16 [ atoms ]
 17 ;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
bond_type
 18  1   c3 1   UNKC11-0.095100 12.01000   c3
 0.11670012.01000
 19  2   c3 1   UNKC22-0.095100 12.01000   oh
-0.59880112.01000
 20  3   hc 1   UNKH13 0.031700  1.00800   h1
 0.028700 1.00800
 21  4   hc 1   UNKH24 0.031700  1.00800   h1
 0.028700 1.00800
 22  5   hc 1   UNKH35 0.031700  1.00800   h1
 0.028700 1.00800
 23  6   hc 1   UNKH46 0.031700  1.00800   ho
 0.396000 1.00800
 24  7   hc 1   UNKH57 0.031700  1.00800   dh
 0.00 1.00800
 25  8   hc 1   UNKH68 0.031700  1.00800   dh
 0.00 1.00800
 26
 27 [ bonds ]
 28 ;   ai aj funct   r k
 29  1  2   11.5375e-012.5179e+05  1.4233e-012.6501e+05
 30  1  3   11.0969e-012.7665e+05  1.0969e-012.7665e+05
 31  1  4   11.0969e-012.7665e+05  1.0969e-012.7665e+05
 32  1  5   11.0969e-012.7665e+05  1.0969e-012.7665e+05
 33  2  6   11.0969e-012.7665e+05  9.7300e-023.1079e+05
 34  2  7   11.0969e-012.7665e+05  1.0969e-012.7665e+05
 35  2  8   11.0969e-012.7665e+05  1.0969e-012.7665e+05
...
..."

I know to perturbing from large molecule(ethane) to small(methanol), I need
to perturb the electrostatic interaction first than vdw, But I don't know
where to perturb the bonded lambdas. I have tested different orders of
Bonded lambdas, and I have got a quite different answer which seems odd to
me. I have a table for that
stage1 stage2 stage3 dG(kj) dG(kcal)
single topology solv q/bonded/vdw -14.36 -3.43
bonded q vdw -13.79 -3.30
bonded/q vdw -14.91 -3.56
q bonded vdw -17.13 -4.09
q bonded/vdw -20.22 -4.83
q vdw bonded -25.2 -6.02
single topology vac q/bonded/vdw 10.32 2.47
bonded q vdw 9.53 2.28
bonded/q vdw 9.1 2.17
q bonded vdw 8.71 2.08
q bonded/vdw 9.64 2.30
q vdw bonded 9.84 2.35
The desolvation free energy of ethane is -2.48 and methanol 3.48kcal.
The best result which close the cyclo for ethane,vac -> ethane, solv ->
methanol, solv -> methanol,vac -> ethane,vac is perturbing all three
together(q/bonded/vdw) followed by perturbing bonded/q together then vdw.
The worst is to decouple bonded lambdas the last. When I try dual topology
method, there is no such difference where to place the bonded lambdas...

 I am confused that which one should used and why others are not OK?

Thank you
Best
Peng
--
Gromacs Users mailing list

* Please search the archive at  
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before  
posting!


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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users  
or send a mail to gmx-users-requ...@gromacs.org.




--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] question of perturbing order in single topology FEP, gromacs

[Peng He]

HI, all,

I am recently doing some test FEP calculations to get familiar, I am
preparing a system of ethane -> methanol using Amber gaff force field and
single topology method.

"  4 [ atomtypes ]
  5 ;name   bond_type mass charge   ptype   sigma epsilon
Amb
  6  c3   c3  0.0  0.0   A 3.39967e-01
4.57730e-01 ; 1.91  0.1094
  7  hc   hc  0.0  0.0   A 2.64953e-01
6.56888e-02 ; 1.49  0.0157
  8  oh   oh  0.0  0.0   A 3.06647e-01
8.80314e-01 ; 1.72  0.2104
  9  h1   h1  0.0  0.0   A 2.47135e-01
6.56888e-02 ; 1.39  0.0157
 10  dh   hc  0.0  0.0   A 0.0  0.0
 11  ho   ho  0.0  0.0   A 0.0e+00   0.0e+00
 12 [ moleculetype ]
 13 ;namenrexcl
 14  UNK  3
 15
 16 [ atoms ]
 17 ;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot
bond_type
 18  1   c3 1   UNKC11-0.095100 12.01000   c3
 0.11670012.01000
 19  2   c3 1   UNKC22-0.095100 12.01000   oh
-0.59880112.01000
 20  3   hc 1   UNKH13 0.031700  1.00800   h1
 0.028700 1.00800
 21  4   hc 1   UNKH24 0.031700  1.00800   h1
 0.028700 1.00800
 22  5   hc 1   UNKH35 0.031700  1.00800   h1
 0.028700 1.00800
 23  6   hc 1   UNKH46 0.031700  1.00800   ho
 0.396000 1.00800
 24  7   hc 1   UNKH57 0.031700  1.00800   dh
 0.00 1.00800
 25  8   hc 1   UNKH68 0.031700  1.00800   dh
 0.00 1.00800
 26
 27 [ bonds ]
 28 ;   ai aj funct   r k
 29  1  2   11.5375e-012.5179e+05  1.4233e-012.6501e+05
 30  1  3   11.0969e-012.7665e+05  1.0969e-012.7665e+05
 31  1  4   11.0969e-012.7665e+05  1.0969e-012.7665e+05
 32  1  5   11.0969e-012.7665e+05  1.0969e-012.7665e+05
 33  2  6   11.0969e-012.7665e+05  9.7300e-023.1079e+05
 34  2  7   11.0969e-012.7665e+05  1.0969e-012.7665e+05
 35  2  8   11.0969e-012.7665e+05  1.0969e-012.7665e+05
...
..."

I know to perturbing from large molecule(ethane) to small(methanol), I need
to perturb the electrostatic interaction first than vdw, But I don't know
where to perturb the bonded lambdas. I have tested different orders of
Bonded lambdas, and I have got a quite different answer which seems odd to
me. I have a table for that
stage1 stage2 stage3 dG(kj) dG(kcal)
single topology solv q/bonded/vdw -14.36 -3.43
bonded q vdw -13.79 -3.30
bonded/q vdw -14.91 -3.56
q bonded vdw -17.13 -4.09
q bonded/vdw -20.22 -4.83
q vdw bonded -25.2 -6.02
single topology vac q/bonded/vdw 10.32 2.47
bonded q vdw 9.53 2.28
bonded/q vdw 9.1 2.17
q bonded vdw 8.71 2.08
q bonded/vdw 9.64 2.30
q vdw bonded 9.84 2.35
The desolvation free energy of ethane is -2.48 and methanol 3.48kcal.
The best result which close the cyclo for ethane,vac -> ethane, solv ->
methanol, solv -> methanol,vac -> ethane,vac is perturbing all three
together(q/bonded/vdw) followed by perturbing bonded/q together then vdw.
The worst is to decouple bonded lambdas the last. When I try dual topology
method, there is no such difference where to place the bonded lambdas...

 I am confused that which one should used and why others are not OK?

Thank you
Best
Peng
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Changing tau_p for parrinello-rahman made my simulation stable

[Mark Abraham]

Hi

If I faced any issues, then I would use Berendsen NPT until the volume
stabliized, rather than making arbitrary choices of lengths of time for
phases. One is trying to equilibrate, so looking at the longest-timescale
relevant observables makes some sense.

Mark

On Wed, Nov 29, 2017 at 6:05 PM Hermann, Johannes <
j.herm...@lrz.tu-muenchen.de> wrote:

> Hi Mark,
>
> thank you for your reply. So you would not recommend using tau_p=2.0?
>
> I did EM, Annealing (1ns), NVT (1ns), NPT (1ns), and then the simulation
> crashes after 15 ns.
>
> So would you recommend like 10 ns with Berendsen after NPT? Crashing
> after 15ns could still due to not being in equilibrium?
>
> Thanks in advance!
>
> All the best
>
> Johannes
>
>
> On 29.11.2017 17:52, Mark Abraham wrote:
> > Hi,
> >
> > P-R is well known to be unsuitable for systems that are not yet close to
> > equilibrium, and documented accordingly.
> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up also
> suggests
> > this might be an idea to avoid. Recent versions of grompp even warn if
> you
> > use that together with generating new velocities. So start with Berendsen
> > and then switch.
> >
> > Mark
> >
> > On Wed, Nov 29, 2017 at 5:28 PM Hermann, Johannes <
> > j.herm...@lrz.tu-muenchen.de> wrote:
> >
> >> Dear all,
> >>
> >> I had a hard time making my simulation stable. Perhaps someone has an
> >> explanation, perhaps it (just) saves someone a lot of time. However, I
> >> want to share my experience:
> >>
> >> I have a dense simulation box (80% water, 20% protein). Free simulation,
> >> no restrains, constrains on the H-bonds. After some time (around 15ns) I
> >> always get LINCS warnings, which lead the simulation to stop either
> >> because of a "Segmentation fault (11)" or "1 particles communicated to
> >> PME rank 0 are more than 2/3 times the cut-off..". I looked at the
> >> trajectories but could not identify any strange behavior.
> >>
> >> I tried a lot of things, but what made my simulations eventually stable
> >> was to increase tau_p for parrinello-rahman from 1.0 to 2.0. Can it be
> >> guessed whether this value is okay, or will it produce un-physical
> >> behavior?
> >>
> >> I know I did not provide a lot of specifics about my setup and run
> >> parameters, I can happily provide that if someone wants to dig deeper
> that.
> >>
> >> All the best
> >>
> >> Johannes
> >>
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
>
> --
> __
> *Technische Universität München*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl für Bioverfahrenstechnik
> Boltzmannstr. 15
> D-85748 Garching
> Tel: +49 8928915730 <+49%2089%2028915730>
> Fax: +49 8928915714 <+49%2089%2028915714>
>
> Email: j.herm...@lrz.tum.de
> http://www.biovt.mw.tum.de/
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Changing tau_p for parrinello-rahman made my simulation stable

[Hermann, Johannes]

Hi Mark,

thank you for your reply. So you would not recommend using tau_p=2.0?

I did EM, Annealing (1ns), NVT (1ns), NPT (1ns), and then the simulation 
crashes after 15 ns.


So would you recommend like 10 ns with Berendsen after NPT? Crashing 
after 15ns could still due to not being in equilibrium?


Thanks in advance!

All the best

Johannes


On 29.11.2017 17:52, Mark Abraham wrote:

Hi,

P-R is well known to be unsuitable for systems that are not yet close to
equilibrium, and documented accordingly.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up also suggests
this might be an idea to avoid. Recent versions of grompp even warn if you
use that together with generating new velocities. So start with Berendsen
and then switch.

Mark

On Wed, Nov 29, 2017 at 5:28 PM Hermann, Johannes <
j.herm...@lrz.tu-muenchen.de> wrote:


Dear all,

I had a hard time making my simulation stable. Perhaps someone has an
explanation, perhaps it (just) saves someone a lot of time. However, I
want to share my experience:

I have a dense simulation box (80% water, 20% protein). Free simulation,
no restrains, constrains on the H-bonds. After some time (around 15ns) I
always get LINCS warnings, which lead the simulation to stop either
because of a "Segmentation fault (11)" or "1 particles communicated to
PME rank 0 are more than 2/3 times the cut-off..". I looked at the
trajectories but could not identify any strange behavior.

I tried a lot of things, but what made my simulations eventually stable
was to increase tau_p for parrinello-rahman from 1.0 to 2.0. Can it be
guessed whether this value is okay, or will it produce un-physical
behavior?

I know I did not provide a lot of specifics about my setup and run
parameters, I can happily provide that if someone wants to dig deeper that.

All the best

Johannes


--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.



--
__
*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.herm...@lrz.tum.de
http://www.biovt.mw.tum.de/

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Can I attach two (or more) (Langevin) thermostats to one atom (or tc-group)?

[Mark Abraham]

Hi,

No there's no support for this. I would strongly suggest using a more
recent version of GROMACS, so that you get to benefit from the 6+ years of
fixed bugs also ;-)

Mark

On Wed, Nov 29, 2017 at 5:20 PM Lovuit CHEN  wrote:

> Dear all,
>
> I am doing MD simulation for comparatively smaller systems with Gromacs
> (older version of 4.5.5). I know you are allowed to attach one thermostat
> to each temperature coupling group you've assigned, with a particular
> "ref-t" and "tau-t" valuable. But I am testing the bath models, so my
> question is can I attach two or more Langevin-type stochastic thermostats
> to only one group (or one atom) at the same time. Theoretically, it would
> be just a change to the equation of motion, but I don't know if it can be
> achieved by only changing the topology inputs. Or maybe one has to change
> the source code a bit?
>
> Any suggestions will be helpful.
>
> Thank you very much in advance!
>
>
> Lovuit
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Changing tau_p for parrinello-rahman made my simulation stable

[Mark Abraham]

Hi,

P-R is well known to be unsuitable for systems that are not yet close to
equilibrium, and documented accordingly.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up also suggests
this might be an idea to avoid. Recent versions of grompp even warn if you
use that together with generating new velocities. So start with Berendsen
and then switch.

Mark

On Wed, Nov 29, 2017 at 5:28 PM Hermann, Johannes <
j.herm...@lrz.tu-muenchen.de> wrote:

> Dear all,
>
> I had a hard time making my simulation stable. Perhaps someone has an
> explanation, perhaps it (just) saves someone a lot of time. However, I
> want to share my experience:
>
> I have a dense simulation box (80% water, 20% protein). Free simulation,
> no restrains, constrains on the H-bonds. After some time (around 15ns) I
> always get LINCS warnings, which lead the simulation to stop either
> because of a "Segmentation fault (11)" or "1 particles communicated to
> PME rank 0 are more than 2/3 times the cut-off..". I looked at the
> trajectories but could not identify any strange behavior.
>
> I tried a lot of things, but what made my simulations eventually stable
> was to increase tau_p for parrinello-rahman from 1.0 to 2.0. Can it be
> guessed whether this value is okay, or will it produce un-physical
> behavior?
>
> I know I did not provide a lot of specifics about my setup and run
> parameters, I can happily provide that if someone wants to dig deeper that.
>
> All the best
>
> Johannes
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Changing tau_p for parrinello-rahman made my simulation stable

[Hermann, Johannes]

Dear all,

I had a hard time making my simulation stable. Perhaps someone has an 
explanation, perhaps it (just) saves someone a lot of time. However, I 
want to share my experience:


I have a dense simulation box (80% water, 20% protein). Free simulation, 
no restrains, constrains on the H-bonds. After some time (around 15ns) I 
always get LINCS warnings, which lead the simulation to stop either 
because of a "Segmentation fault (11)" or "1 particles communicated to 
PME rank 0 are more than 2/3 times the cut-off..". I looked at the 
trajectories but could not identify any strange behavior.


I tried a lot of things, but what made my simulations eventually stable 
was to increase tau_p for parrinello-rahman from 1.0 to 2.0. Can it be 
guessed whether this value is okay, or will it produce un-physical behavior?


I know I did not provide a lot of specifics about my setup and run 
parameters, I can happily provide that if someone wants to dig deeper that.


All the best

Johannes


--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Can I attach two (or more) (Langevin) thermostats to one atom (or tc-group)?

[Lovuit CHEN]

Dear all,

I am doing MD simulation for comparatively smaller systems with Gromacs (older 
version of 4.5.5). I know you are allowed to attach one thermostat to each 
temperature coupling group you've assigned, with a particular "ref-t" and 
"tau-t" valuable. But I am testing the bath models, so my question is can I 
attach two or more Langevin-type stochastic thermostats to only one group (or 
one atom) at the same time. Theoretically, it would be just a change to the 
equation of motion, but I don't know if it can be achieved by only changing the 
topology inputs. Or maybe one has to change the source code a bit?

Any suggestions will be helpful.

Thank you very much in advance!


Lovuit
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] gmx distance,umbrella sampling

[rose rahmani]

Hello;

would you please tell me how gmx distance calculate and write COM distance
from .gro and .tpr files excactly?


Best regards
-Rose
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Average data files with gmx analyze

[mario]

Dear Justin:
thank you very much!
best regards!
Mario Campo

>
>
> On 11/29/17 4:35 AM, ma...@exactas.unlpam.edu.ar wrote:
>> Dear GROMACS developers:
>> The gmx tutorial tells me that in order to average data from columns of
>> several similar files XVG, I must use gmx analize
>> "gmx analyze reads an ASCII file and analyzes data sets. ... Multiple
>> sets
>> can also be read when they are separated by & (option -n); in this case
>> only one y-value is read from each line..."
>> (http://manual.gromacs.org/programs/gmx-analyze.html)
>>
>> But the indication does not seem clear.
>>
>> I try to average data from den1.xvg, den2.xvg etc files
>>
>> I already tried, among other things, this sequence of indications and it
>> does not work:
>> gmx analyze -f den1.xvg & den2.xvg -n 2 -av
>>
>> Could you tell me what I'm doing wrong?
>
> The description refers to multiple data sets in a single file, separated
> by &, as is produced by several GROMACS programs.
>
> @set1
> x1 y1
> x2 y2
> ...
> &
> @set2
> x1 y1
> x2 y2
> ...
>
> You cannot pass multiple files to gmx analyze via -f, and certainly not
> with &.
>
> -Justin
>
>> (I add the answer in terminal (summarized)):
>>
>> GROMACS:  gmx analyze, VERSION 5.1.2
>> Executable:   /usr/bin/gmx
>> Data prefix:  /usr
>> Command line:
>>gmx analyze -f den1.xvg
>>
>> Read 1 sets of 5001 points, dt = 2
>>
>>std. dev.relative deviation
>> of
>> standard   -   cumulants from those
>> of
>> set  average   deviation  sqrt(n-1)   a Gaussian
>> distribition
>>cum. 3   cum. 4
>> SS1   1.683733e+01   1.830422e-01   2.588608e-03   0.047   -0.045
>>
>>
>> gcq#433: "If you want to save your child from polio, you can pray or you
>> can inoculate... choose science." (Carl Sagan)
>>
>> den2.xvg: no se encontró la orden
>> [1]+  Hecho   gmx analyze -f den1.xvg
>>
>>
>>
>
> --
> ==
>
> 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
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
> a mail to gmx-users-requ...@gromacs.org.


-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Average data files with gmx analyze

[Justin Lemkul]

On 11/29/17 4:35 AM, ma...@exactas.unlpam.edu.ar wrote:

Dear GROMACS developers:
The gmx tutorial tells me that in order to average data from columns of
several similar files XVG, I must use gmx analize
"gmx analyze reads an ASCII file and analyzes data sets. ... Multiple sets
can also be read when they are separated by & (option -n); in this case
only one y-value is read from each line..."
(http://manual.gromacs.org/programs/gmx-analyze.html)

But the indication does not seem clear.

I try to average data from den1.xvg, den2.xvg etc files

I already tried, among other things, this sequence of indications and it
does not work:
gmx analyze -f den1.xvg & den2.xvg -n 2 -av

Could you tell me what I'm doing wrong?


The description refers to multiple data sets in a single file, separated 
by &, as is produced by several GROMACS programs.


@set1
x1 y1
x2 y2
...
&
@set2
x1 y1
x2 y2
...

You cannot pass multiple files to gmx analyze via -f, and certainly not 
with &.


-Justin


(I add the answer in terminal (summarized)):

GROMACS:  gmx analyze, VERSION 5.1.2
Executable:   /usr/bin/gmx
Data prefix:  /usr
Command line:
   gmx analyze -f den1.xvg

Read 1 sets of 5001 points, dt = 2

   std. dev.relative deviation of
standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
   cum. 3   cum. 4
SS1   1.683733e+01   1.830422e-01   2.588608e-03   0.047   -0.045


gcq#433: "If you want to save your child from polio, you can pray or you
can inoculate... choose science." (Carl Sagan)

den2.xvg: no se encontró la orden
[1]+  Hecho   gmx analyze -f den1.xvg





--
==

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

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Average data files with gmx analyze

[mario]

Dear GROMACS developers:
The gmx tutorial tells me that in order to average data from columns of
several similar files XVG, I must use gmx analize
"gmx analyze reads an ASCII file and analyzes data sets. ... Multiple sets
can also be read when they are separated by & (option -n); in this case
only one y-value is read from each line..."
(http://manual.gromacs.org/programs/gmx-analyze.html)

But the indication does not seem clear.

I try to average data from den1.xvg, den2.xvg etc files

I already tried, among other things, this sequence of indications and it
does not work:
gmx analyze -f den1.xvg & den2.xvg -n 2 -av

Could you tell me what I'm doing wrong?

(I add the answer in terminal (summarized)):

GROMACS:  gmx analyze, VERSION 5.1.2
Executable:   /usr/bin/gmx
Data prefix:  /usr
Command line:
  gmx analyze -f den1.xvg

Read 1 sets of 5001 points, dt = 2

  std. dev.relative deviation of
   standard   -   cumulants from those of
set  average   deviation  sqrt(n-1)   a Gaussian distribition
  cum. 3   cum. 4
SS1   1.683733e+01   1.830422e-01   2.588608e-03   0.047   -0.045


gcq#433: "If you want to save your child from polio, you can pray or you
can inoculate... choose science." (Carl Sagan)

den2.xvg: no se encontró la orden
[1]+  Hecho   gmx analyze -f den1.xvg



-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Acetylated histone with DNA

[Justin Lemkul]

On 11/29/17 4:22 AM, Mehreen Jan wrote:

Hello

Hope all will be fine

  I have acetylated the lysine from Vienna PTM server using 54a8 force field. 
Lysine was successfully acetylated (KAC).I have simulated the acetylated 
protein by uisng 54a8ff downloaded from Vienna PTM and the expeiment was 
successful at 1ns. Now we want to simulate acetylated protein with DNA, as 
there is no combine force field. We modify the amber99bsc1ff by copying the 
parameters of KAC form 54a8 force feild,we got following error:
 :the atom type CH1 (residue KAC) notfound in 
atom type database'.
one more thing if we delete CH1 the acetylated lysine was completely deleted. 
can any one help me by suggesting me the force field having combine parametres 
for both.


CHARMM36 can handle this. The acetylated lysine residue is called ALY. 
For some reason, it's not in the GROMACS port of the force field, but 
you can find it in the CHARMM distribution in 
stream/prot/toppar_all36_prot_modify_res.str (RESI ALY). Just create a 
new .rtp entry based on LYS and add it to residuetypes.dat.


-Justin

--
==

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

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

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

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Metal-Protein interactions

[RAHUL SURESH]

Thank you Justin.

It was helpful

On Wed, Nov 29, 2017 at 7:33 AM, Justin Lemkul  wrote:

>
>
> On 11/28/17 1:00 PM, RAHUL SURESH wrote:
>
>> On Tue, 28 Nov 2017 at 7:14 PM, Justin Lemkul  wrote:
>>
>>
>>> On 11/28/17 4:54 AM, RAHUL SURESH wrote:
>>>
 I am trying to simulate a metal-protein interaction using gromacs 2016
 package and charmm36 ff.
 I have prepared the initial pdb by performing an oniom calculations

>>> between
>>>
 protein and metal (at various positions) using gaussian 09 and chose the
 structure with maximum binding energy. The metal ion is bonded to oxygen
 atom of His residue. Having a look at gro file after each step

>>> That's unusual; His typically coordinate metals via their delta or
>>> epsilon N atoms.
>>>
>>> Sorry that I pronounced wrongly as oxygen.. regret the inconvenience.
>>
>> (protein.gro, em.gro, nvt.groand npt.gro) the distance between metal  ion
 and the oxygen atom keeps increasing starting from 2.06 to 2.69. Over
 the
 course of simulations for 10ns, the metal ion is away from the protein.

 What can be done to have the metal ion restrained at its position? Or if

>>> I
>>>
 extend the simulation will the metal ion find its appropritae position
 during the course time?

>>> Unlikely. This is a fundamental issue with classical mechanical force
>>> fields approximating ion interactions very poorly, particularly in the
>>> case of multivalent and/or transition metals. There are many effects
>>> like polarization and charge transfer that simply can't be modeled. You
>>> can apply distance restraints (or actual covalent bonds), NBFIX LJ
>>> parameters, etc.
>>>
>> while restraing the metal ion, it arise an error stating that an atom can
>> not be mentioned in two groups.
>> Tc grps = protein_cu water_and_ions.
>> Cu will already be mentioned in ions.
>>
>
> It should be grouped with the protein; a coordinated metal is functionally
> part of the protein and should be treated as such. It makes no sense to
> couple it to the solvent thermostat.
>
> and that may be enough to preserve the binding pose. In
>>
>>> reality, one would have to reparametrize any ligating residues because
>>> the charge distribution on the ion and anything coordinating it is not
>>> at all what the standard force field uses.
>>>
>> Reparameterize.? Means I have to add additional parameter file to the
>> charmm36 ff after interacting with metal ion.?
>>
>
> It means you would have to derive new residue definitions, but a QM/MM
> approach is probably superior.
>
>
>> Also Justin, what if I can manually add a bond between N of HIS and metal
>> ion with most appropriate bond length ..?
>> (To avoid complexity if it works)
>>
>
> Yes, that is a possibility, but again you will have to do some QM work to
> properly parametrize the geometries and vibrational frequencies for the new
> bonded parameters (which then include angles and dihedrals). Cu2+ is a
> difficult ion to deal with, though, so this may be surprisingly laborious.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Acetylated histone with DNA

[Mehreen Jan]

Hello

Hope all will be fine

 I have acetylated the lysine from Vienna PTM server using 54a8 force field. 
Lysine was successfully acetylated (KAC).I have simulated the acetylated 
protein by uisng 54a8ff downloaded from Vienna PTM and the expeiment was 
successful at 1ns. Now we want to simulate acetylated protein with DNA, as 
there is no combine force field. We modify the amber99bsc1ff by copying the 
parameters of KAC form 54a8 force feild,we got following error:
:the atom type CH1 (residue KAC) notfound in 
atom type database'.
one more thing if we delete CH1 the acetylated lysine was completely deleted. 
can any one help me by suggesting me the force field having combine parametres 
for both.
thank you in advanced 

Mehreen Jan
from Pakistan
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.