Re: [gmx-users] I have questions for tabulated bonded potentials

[Chang Woon Jang]

Dear Justin Lemkul,

  I got it. Thank you very much for your help.

Best regards,
Changwoon Jang

On Tue, Aug 30, 2016 at 8:40 PM, Chang Woon Jang 
wrote:

> Dear Justin,
>
>
>Do you mean "Order of parameters"? If I would like to specify for
> table_b1.xvg, I need to set 1 after 8. If I would like to specifiy for
> table_b2.xvg, I need to set 2 after 8.
>
> Am I right?
>
> Best regards,
> Changwoon Jang
>
> On Tue, Aug 30, 2016 at 8:35 PM, Chang Woon Jang 
> wrote:
>
>> Dear Justin Lemkul,
>>
>> I have seen the 4.2.12 and Table 5.5. However, it does not show the
>> specific example for several tabulated potentials in topol.top file. I
>> created table_b1.xvg, table_b2.xvg ... table_b5.xvg, table_a1.xvg,
>> table_a2.xvg ... table_a6.xvg, table_d1.xvg  table_d4.xvg. Those are
>> different n values for each interactions.
>>
>> However, 4.2.12 just says that "Multiple tables can be supplied simply by
>> using different values of n, and are applied to the appropriate bonds, as
>> specified in the topology (Table 5.5)".
>>
>> In Table 5.5, tabulated bond funct is specified with 8 or 9, but there is
>> no explanation for distingushing several tables to specify different bonded
>> interactions.
>>
>> Thank you.
>>
>> Best regards,
>> Changwoon Jang
>>
>> On Tue, Aug 30, 2016 at 8:19 PM, Justin Lemkul  wrote:
>>
>>>
>>>
>>> On 8/30/16 8:11 PM, Chang Woon Jang wrote:
>>>
 Dear Gromacs Users,

   From the above question, I think that I need to specify the each
 bonded interaction in topol.top file. Am I right?

For example,


 [ bond ]
 1  1  2  table_b1.xvg
 2  2  3  table_b2.xvg
 3  3  4  table_b3.xvg


 Is this right format if I have several tabulated potential files in
 topol.top?


>>> No.  Consult Table 5.5 - the function type is 8 (or 9, depending on
>>> whether you need to generate exclusions) and the table number is supplied
>>> as one of the parameters.  See also section 4.2.14.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * 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.
>>>
>>
>>
>>
>> --
>> Best regards,
>> Changwoon Jang,
>>
>> Postdoctoral Research Fellow
>> Department of Chemical & Biological Engineering, Drexel University
>> 3141 Chestnut Street, Philadelphia, PA 19104
>>
>> Voice: (662) 617-2267
>> E-mail: cj...@drexel.edu
>>
>
>
>
> --
>
>
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Re: [gmx-users] I have questions for tabulated bonded potentials

[Chang Woon Jang]

Dear Justin,


   Do you mean "Order of parameters"? If I would like to specify for
table_b1.xvg, I need to set 1 after 8. If I would like to specifiy for
table_b2.xvg, I need to set 2 after 8.

Am I right?

Best regards,
Changwoon Jang

On Tue, Aug 30, 2016 at 8:35 PM, Chang Woon Jang 
wrote:

> Dear Justin Lemkul,
>
> I have seen the 4.2.12 and Table 5.5. However, it does not show the
> specific example for several tabulated potentials in topol.top file. I
> created table_b1.xvg, table_b2.xvg ... table_b5.xvg, table_a1.xvg,
> table_a2.xvg ... table_a6.xvg, table_d1.xvg  table_d4.xvg. Those are
> different n values for each interactions.
>
> However, 4.2.12 just says that "Multiple tables can be supplied simply by
> using different values of n, and are applied to the appropriate bonds, as
> specified in the topology (Table 5.5)".
>
> In Table 5.5, tabulated bond funct is specified with 8 or 9, but there is
> no explanation for distingushing several tables to specify different bonded
> interactions.
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
> On Tue, Aug 30, 2016 at 8:19 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 8/30/16 8:11 PM, Chang Woon Jang wrote:
>>
>>> Dear Gromacs Users,
>>>
>>>   From the above question, I think that I need to specify the each
>>> bonded interaction in topol.top file. Am I right?
>>>
>>>For example,
>>>
>>>
>>> [ bond ]
>>> 1  1  2  table_b1.xvg
>>> 2  2  3  table_b2.xvg
>>> 3  3  4  table_b3.xvg
>>>
>>>
>>> Is this right format if I have several tabulated potential files in
>>> topol.top?
>>>
>>>
>> No.  Consult Table 5.5 - the function type is 8 (or 9, depending on
>> whether you need to generate exclusions) and the table number is supplied
>> as one of the parameters.  See also section 4.2.14.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> Gromacs Users mailing list
>>
>> * 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.
>>
>
>
>
> --
> Best regards,
> Changwoon Jang,
>
> Postdoctoral Research Fellow
> Department of Chemical & Biological Engineering, Drexel University
> 3141 Chestnut Street, Philadelphia, PA 19104
>
> Voice: (662) 617-2267
> E-mail: cj...@drexel.edu
>



-- 
Best regards,
Changwoon Jang,

Postdoctoral Research Fellow
Department of Chemical & Biological Engineering, Drexel University
3141 Chestnut Street, Philadelphia, PA 19104

Voice: (662) 617-2267
E-mail: cj...@drexel.edu
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Re: [gmx-users] I have questions for tabulated bonded potentials

[Justin Lemkul]

On 8/30/16 8:35 PM, Chang Woon Jang wrote:

Dear Justin Lemkul,

I have seen the 4.2.12 and Table 5.5. However, it does not show the
specific example for several tabulated potentials in topol.top file. I
created table_b1.xvg, table_b2.xvg ... table_b5.xvg, table_a1.xvg,
table_a2.xvg ... table_a6.xvg, table_d1.xvg  table_d4.xvg. Those are
different n values for each interactions.

However, 4.2.12 just says that "Multiple tables can be supplied simply by
using different values of n, and are applied to the appropriate bonds, as
specified in the topology (Table 5.5)".

In Table 5.5, tabulated bond funct is specified with 8 or 9, but there is
no explanation for distingushing several tables to specify different bonded
interactions.



In section 4.2.14:

"For each interaction, the force constant k and the table number n are specified 
in the topology."


In Table 5.5 (in the column "Order of parameters and their units"):

table number (≥ 0); k (kJ mol−1)

So for table_b1.xvg with k = 1000 (just an example) to be applied to atoms 1 
and 2:

[ bonds ]
; ai aj func table k
  1   2   8   11000

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] I have questions for tabulated bonded potentials

[Chang Woon Jang]

Dear Justin Lemkul,

I have seen the 4.2.12 and Table 5.5. However, it does not show the
specific example for several tabulated potentials in topol.top file. I
created table_b1.xvg, table_b2.xvg ... table_b5.xvg, table_a1.xvg,
table_a2.xvg ... table_a6.xvg, table_d1.xvg  table_d4.xvg. Those are
different n values for each interactions.

However, 4.2.12 just says that "Multiple tables can be supplied simply by
using different values of n, and are applied to the appropriate bonds, as
specified in the topology (Table 5.5)".

In Table 5.5, tabulated bond funct is specified with 8 or 9, but there is
no explanation for distingushing several tables to specify different bonded
interactions.

Thank you.

Best regards,
Changwoon Jang

On Tue, Aug 30, 2016 at 8:19 PM, Justin Lemkul  wrote:

>
>
> On 8/30/16 8:11 PM, Chang Woon Jang wrote:
>
>> Dear Gromacs Users,
>>
>>   From the above question, I think that I need to specify the each
>> bonded interaction in topol.top file. Am I right?
>>
>>For example,
>>
>>
>> [ bond ]
>> 1  1  2  table_b1.xvg
>> 2  2  3  table_b2.xvg
>> 3  3  4  table_b3.xvg
>>
>>
>> Is this right format if I have several tabulated potential files in
>> topol.top?
>>
>>
> No.  Consult Table 5.5 - the function type is 8 (or 9, depending on
> whether you need to generate exclusions) and the table number is supplied
> as one of the parameters.  See also section 4.2.14.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * 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.
>



-- 
Best regards,
Changwoon Jang,

Postdoctoral Research Fellow
Department of Chemical & Biological Engineering, Drexel University
3141 Chestnut Street, Philadelphia, PA 19104

Voice: (662) 617-2267
E-mail: cj...@drexel.edu
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Re: [gmx-users] I have questions for tabulated bonded potentials

[Justin Lemkul]

On 8/30/16 8:11 PM, Chang Woon Jang wrote:

Dear Gromacs Users,

  From the above question, I think that I need to specify the each
bonded interaction in topol.top file. Am I right?

   For example,


[ bond ]
1  1  2  table_b1.xvg
2  2  3  table_b2.xvg
3  3  4  table_b3.xvg


Is this right format if I have several tabulated potential files in
topol.top?



No.  Consult Table 5.5 - the function type is 8 (or 9, depending on whether you 
need to generate exclusions) and the table number is supplied as one of the 
parameters.  See also section 4.2.14.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] I have questions for tabulated bonded potentials

[Chang Woon Jang]

Dear Gromacs Users,

  From the above question, I think that I need to specify the each
bonded interaction in topol.top file. Am I right?

   For example,


[ bond ]
1  1  2  table_b1.xvg
2  2  3  table_b2.xvg
3  3  4  table_b3.xvg


Is this right format if I have several tabulated potential files in
topol.top?

Thank you.

Best regards,
Changwoon Jang




On Tue, Aug 30, 2016 at 4:31 PM, Chang Woon Jang 
wrote:

> Dear Gromacs Users,
>
> I have several bond, angle, dihedral potentials named table_b1.xvg,
> table_b2.xvg, table_b3.xvg ...table_a1.xvg, table_a2.xvg ... table_d1.xvg,
> table_d2.xvg, table_d3.xvg, table_d4.xvg.
>
> In my system, there are 6 types of beads (A, B, C, D, E, F). How can I
> assign each potential table to specific interactions. For example,
> table_b1.xvg is A-B bond interaction, table_a1.xvg is A-B-A angle
> interactions end so on.
>
> Thank you.
>
>
> Best regards,
> Changwoon Jang,
>
>
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[gmx-users] Normal Mode Analysis failing with no error message

[jhon espinosa]

Hi all


I am trying to do a Normal Mode Analysis on a protein assembly with 1.05 
million atoms

without solvent or ions. I ma trying to do so using Gromacs 5.0.4 double 
precision

using 1024 processor and up to 256 GB of RAM, but it always fails.

I do not get any error message from Gromacs in just finished.

The last lines of my error log file are:


starting normal mode calculation 'GRoups of Organic Molecules in ACtion for 
Science in water'
2114424 steps.

Maximum force: 1.59067e+03
The force is probably not small enough to ensure that you are at a minimum.
Be aware that negative eigenvalues may occur
when the resulting matrix is diagonalized.

[NID 00841] 2016-08-30 16:36:59 Apid 6732636: initiated application termination
[NID 00841] 2016-08-30 16:37:01 Apid 6732636: OOM killer terminated this 
process.

Any suggestion

Michael

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[gmx-users] I have questions for tabulated bonded potentials

[Chang Woon Jang]

Dear Gromacs Users,

I have several bond, angle, dihedral potentials named table_b1.xvg,
table_b2.xvg, table_b3.xvg ...table_a1.xvg, table_a2.xvg ... table_d1.xvg,
table_d2.xvg, table_d3.xvg, table_d4.xvg.

In my system, there are 6 types of beads (A, B, C, D, E, F). How can I
assign each potential table to specific interactions. For example,
table_b1.xvg is A-B bond interaction, table_a1.xvg is A-B-A angle
interactions end so on.

Thank you.


Best regards,
Changwoon Jang,
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Re: [gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

[Chang Woon Jang]

Dear Justin,

 Search engine give a clue about using -nt options. However, how to
choose the proper number for -nt option from the error message?

Thank you.

Best regards,
Changwoon Jang

On Tue, Aug 30, 2016 at 12:02 PM, Justin Lemkul  wrote:

>
>
> On 8/30/16 11:52 AM, Chang Woon Jang wrote:
>
>> Dear Justin Lemkul,
>>
>> Thank you for your answers. The following is the error message after I
>> run " gmx mdrun -s topol.tpr -c confgout.gro -o traj.trr -x traj.xtc -rdd
>> 2.5".
>>
>>
>> Initializing Domain Decomposition on 8 ranks
>> Dynamic load balancing: auto
>> Will sort the charge groups at every domain (re)decomposition
>> Minimum cell size due to bonded interactions: 2.500 nm
>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>> Optimizing the DD grid for 8 cells with a minimum initial size of 3.125 nm
>> The maximum allowed number of cells is: X 1 Y 1 Z 1
>>
>> ---
>> Program gmx, VERSION 5.0.8-dev-20151014-1f04b58
>> Source code file:
>> /home/chang/PACKAGE/votca/src/gromacs/src/gromacs/mdlib/domdec.c, line:
>> 6902
>>
>> Fatal error:
>> There is no domain decomposition for 8 ranks that is compatible with the
>> given box and a minimum cell size of 3.125 nm
>> Change the number of ranks or mdrun option -rdd or -dds
>> Look in the log file for details on the domain decomposition
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>>
>>
> And what does Google tell you about this particular case?  Hint: the same
> error gets posted to this list pretty much weekly, if not more often.  It's
> been rationalized and solved time and time again.
>
> -Justin
>
>
>
>> Best regards,
>> Changwoon Jang
>>
>>
>> On Tue, Aug 30, 2016 at 11:30 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 8/30/16 10:41 AM, Chang Woon Jang wrote:
>>>
>>> Dear Justin Lemkul,
 Thank you for your response. Yes, I use coarse-grained system
 (thermosetting polymer). I prepared the system from the equilibrated
 atomistic system. The atomistic system was equilibrated using OPLS-AA
 force
 filed under NPT and NVT for almost 40 ns. The initial atomistic system
 contained 13854 atoms. The equilibrated atomistic system was
 coarese-grained (mapped) with certain criteria. Now, I am trying to get
 CG
 potentials using iterative Boltzmann Inversion, but this error keeps me
 dizzy.

 Whenever I use -rdd options, it gives another error like domain
 decomposition error with other options recommended. Whenever I use -nt


>>> Please always post exact error messages, copied and pasted directly from
>>> the terminal or .log file.  We can't guess at what you're reading.
>>>
>>> options, the simulation goes well but the simulation trajectory seem
>>> weird
>>>
 that some molecules are going out the simulation box


 This is just PBC.  There is no "outside" of a box.  If you've got
>>> polymers, they will elongate and contract depending on their physical
>>> behavior.  There's nothing wrong with that.
>>>
>>> -Justin
>>>
>>>
>>> It seems tricky to find what is the problem.
>>>

 Thank you.

 Best regards,
 Changwoon Jang

 On Tue, Aug 30, 2016 at 8:37 AM, Justin Lemkul  wrote:



> On 8/29/16 6:02 PM, Chang Woon Jang wrote:
>
> Dear Gromacs Users,
>
>>
>>
>> I have a Fatal error as follow. The error says -rdd option or
>> -ddcheck.
>> How
>> can I properly use these options? Is the following command the proper
>> use
>> of these options?
>>
>> gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -rdd 1.5
>>
>>
>>> -ddcheck
>>>
>>
>>
>> Yes, but note that -ddcheck is on by default anyway, and you should
>> look
>>
> into why this might be happening.  You can get around this error, but
> it
> often indicates instability.  Without a complete description of what
> your
> system is, what you've previously done to prepare, minimize,
> equilibrate,
> etc. we're sort of just guessing here.  If the system is coarse grain,
> then
> use of a large -rdd is typical (as you will see from many threads in
> the
> archive that address this case specifically).
>
> -Justin
>
> Thank you.
>
>
>>
>> 1 of the 1612 bonded interactions could not be calculated because some
>> atoms involved moved further apart than the multi-body cut-off
>> distance
>> (1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd,
>> for
>> pairs and tabulated bonds also see option -ddcheck
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>>
>>
>>

Re: [gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

[Justin Lemkul]

On 8/30/16 11:52 AM, Chang Woon Jang wrote:

Dear Justin Lemkul,

Thank you for your answers. The following is the error message after I
run " gmx mdrun -s topol.tpr -c confgout.gro -o traj.trr -x traj.xtc -rdd
2.5".


Initializing Domain Decomposition on 8 ranks
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Minimum cell size due to bonded interactions: 2.500 nm
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 3.125 nm
The maximum allowed number of cells is: X 1 Y 1 Z 1

---
Program gmx, VERSION 5.0.8-dev-20151014-1f04b58
Source code file:
/home/chang/PACKAGE/votca/src/gromacs/src/gromacs/mdlib/domdec.c, line: 6902

Fatal error:
There is no domain decomposition for 8 ranks that is compatible with the
given box and a minimum cell size of 3.125 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---



And what does Google tell you about this particular case?  Hint: the same error 
gets posted to this list pretty much weekly, if not more often.  It's been 
rationalized and solved time and time again.


-Justin



Best regards,
Changwoon Jang


On Tue, Aug 30, 2016 at 11:30 AM, Justin Lemkul  wrote:




On 8/30/16 10:41 AM, Chang Woon Jang wrote:


Dear Justin Lemkul,
Thank you for your response. Yes, I use coarse-grained system
(thermosetting polymer). I prepared the system from the equilibrated
atomistic system. The atomistic system was equilibrated using OPLS-AA
force
filed under NPT and NVT for almost 40 ns. The initial atomistic system
contained 13854 atoms. The equilibrated atomistic system was
coarese-grained (mapped) with certain criteria. Now, I am trying to get CG
potentials using iterative Boltzmann Inversion, but this error keeps me
dizzy.

Whenever I use -rdd options, it gives another error like domain
decomposition error with other options recommended. Whenever I use -nt



Please always post exact error messages, copied and pasted directly from
the terminal or .log file.  We can't guess at what you're reading.

options, the simulation goes well but the simulation trajectory seem weird

that some molecules are going out the simulation box



This is just PBC.  There is no "outside" of a box.  If you've got
polymers, they will elongate and contract depending on their physical
behavior.  There's nothing wrong with that.

-Justin


It seems tricky to find what is the problem.


Thank you.

Best regards,
Changwoon Jang

On Tue, Aug 30, 2016 at 8:37 AM, Justin Lemkul  wrote:




On 8/29/16 6:02 PM, Chang Woon Jang wrote:

Dear Gromacs Users,



I have a Fatal error as follow. The error says -rdd option or -ddcheck.
How
can I properly use these options? Is the following command the proper
use
of these options?

gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -rdd 1.5



-ddcheck



Yes, but note that -ddcheck is on by default anyway, and you should look

into why this might be happening.  You can get around this error, but it
often indicates instability.  Without a complete description of what your
system is, what you've previously done to prepare, minimize, equilibrate,
etc. we're sort of just guessing here.  If the system is coarse grain,
then
use of a large -rdd is typical (as you will see from many threads in the
archive that address this case specifically).

-Justin

Thank you.




1 of the 1612 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the
GROMACS




Best regards,
Changwoon Jang,


--

==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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==

Justin A. Lemkul, 

Re: [gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

[Chang Woon Jang]

Dear Justin Lemkul,

Thank you for your answers. The following is the error message after I
run " gmx mdrun -s topol.tpr -c confgout.gro -o traj.trr -x traj.xtc -rdd
2.5".


Initializing Domain Decomposition on 8 ranks
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Minimum cell size due to bonded interactions: 2.500 nm
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 3.125 nm
The maximum allowed number of cells is: X 1 Y 1 Z 1

---
Program gmx, VERSION 5.0.8-dev-20151014-1f04b58
Source code file:
/home/chang/PACKAGE/votca/src/gromacs/src/gromacs/mdlib/domdec.c, line: 6902

Fatal error:
There is no domain decomposition for 8 ranks that is compatible with the
given box and a minimum cell size of 3.125 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


Best regards,
Changwoon Jang


On Tue, Aug 30, 2016 at 11:30 AM, Justin Lemkul  wrote:

>
>
> On 8/30/16 10:41 AM, Chang Woon Jang wrote:
>
>> Dear Justin Lemkul,
>> Thank you for your response. Yes, I use coarse-grained system
>> (thermosetting polymer). I prepared the system from the equilibrated
>> atomistic system. The atomistic system was equilibrated using OPLS-AA
>> force
>> filed under NPT and NVT for almost 40 ns. The initial atomistic system
>> contained 13854 atoms. The equilibrated atomistic system was
>> coarese-grained (mapped) with certain criteria. Now, I am trying to get CG
>> potentials using iterative Boltzmann Inversion, but this error keeps me
>> dizzy.
>>
>> Whenever I use -rdd options, it gives another error like domain
>> decomposition error with other options recommended. Whenever I use -nt
>>
>
> Please always post exact error messages, copied and pasted directly from
> the terminal or .log file.  We can't guess at what you're reading.
>
> options, the simulation goes well but the simulation trajectory seem weird
>> that some molecules are going out the simulation box
>>
>>
> This is just PBC.  There is no "outside" of a box.  If you've got
> polymers, they will elongate and contract depending on their physical
> behavior.  There's nothing wrong with that.
>
> -Justin
>
>
> It seems tricky to find what is the problem.
>>
>> Thank you.
>>
>> Best regards,
>> Changwoon Jang
>>
>> On Tue, Aug 30, 2016 at 8:37 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 8/29/16 6:02 PM, Chang Woon Jang wrote:
>>>
>>> Dear Gromacs Users,


 I have a Fatal error as follow. The error says -rdd option or -ddcheck.
 How
 can I properly use these options? Is the following command the proper
 use
 of these options?

 gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -rdd 1.5

>
> -ddcheck


 Yes, but note that -ddcheck is on by default anyway, and you should look
>>> into why this might be happening.  You can get around this error, but it
>>> often indicates instability.  Without a complete description of what your
>>> system is, what you've previously done to prepare, minimize, equilibrate,
>>> etc. we're sort of just guessing here.  If the system is coarse grain,
>>> then
>>> use of a large -rdd is typical (as you will see from many threads in the
>>> archive that address this case specifically).
>>>
>>> -Justin
>>>
>>> Thank you.
>>>


 1 of the 1612 bonded interactions could not be calculated because some
 atoms involved moved further apart than the multi-body cut-off distance
 (1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for
 pairs and tabulated bonds also see option -ddcheck
 For more information and tips for troubleshooting, please check the
 GROMACS




 Best regards,
 Changwoon Jang,


 --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * 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 

Re: [gmx-users] Assigning charges to Proline residues

[Justin Lemkul]

On 8/30/16 11:28 AM, Dan Woodall wrote:

Hello,

I'm looking to define the charges on a 10 residue polypeptide using
pdb2gmx. I want to have the N-terminus charged, and a proline at position 6
charged, but I can only find ways to assign charges to the amino acids that
typically carry charges. Is there a way I can force the program to
recognize a +1 charge (protonated) on a proline?



You need to define a new residue entry in the .rtp file for this specific 
proline type, then assign that new residue name to the residue in the coordinate 
file.  See 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

[Justin Lemkul]

On 8/30/16 10:41 AM, Chang Woon Jang wrote:

Dear Justin Lemkul,
Thank you for your response. Yes, I use coarse-grained system
(thermosetting polymer). I prepared the system from the equilibrated
atomistic system. The atomistic system was equilibrated using OPLS-AA force
filed under NPT and NVT for almost 40 ns. The initial atomistic system
contained 13854 atoms. The equilibrated atomistic system was
coarese-grained (mapped) with certain criteria. Now, I am trying to get CG
potentials using iterative Boltzmann Inversion, but this error keeps me
dizzy.

Whenever I use -rdd options, it gives another error like domain
decomposition error with other options recommended. Whenever I use -nt


Please always post exact error messages, copied and pasted directly from the 
terminal or .log file.  We can't guess at what you're reading.



options, the simulation goes well but the simulation trajectory seem weird
that some molecules are going out the simulation box



This is just PBC.  There is no "outside" of a box.  If you've got polymers, they 
will elongate and contract depending on their physical behavior.  There's 
nothing wrong with that.


-Justin


It seems tricky to find what is the problem.

Thank you.

Best regards,
Changwoon Jang

On Tue, Aug 30, 2016 at 8:37 AM, Justin Lemkul  wrote:




On 8/29/16 6:02 PM, Chang Woon Jang wrote:


Dear Gromacs Users,


I have a Fatal error as follow. The error says -rdd option or -ddcheck.
How
can I properly use these options? Is the following command the proper use
of these options?

gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -rdd 1.5



-ddcheck



Yes, but note that -ddcheck is on by default anyway, and you should look
into why this might be happening.  You can get around this error, but it
often indicates instability.  Without a complete description of what your
system is, what you've previously done to prepare, minimize, equilibrate,
etc. we're sort of just guessing here.  If the system is coarse grain, then
use of a large -rdd is typical (as you will see from many threads in the
archive that address this case specifically).

-Justin

Thank you.



1 of the 1612 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the
GROMACS




Best regards,
Changwoon Jang,



--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Assigning charges to Proline residues

[Dan Woodall]

Hello,

I'm looking to define the charges on a 10 residue polypeptide using
pdb2gmx. I want to have the N-terminus charged, and a proline at position 6
charged, but I can only find ways to assign charges to the amino acids that
typically carry charges. Is there a way I can force the program to
recognize a +1 charge (protonated) on a proline?

Thanks,
Dan
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Re: [gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

[Chang Woon Jang]

Dear Justin Lemkul,
Thank you for your response. Yes, I use coarse-grained system
(thermosetting polymer). I prepared the system from the equilibrated
atomistic system. The atomistic system was equilibrated using OPLS-AA force
filed under NPT and NVT for almost 40 ns. The initial atomistic system
contained 13854 atoms. The equilibrated atomistic system was
coarese-grained (mapped) with certain criteria. Now, I am trying to get CG
potentials using iterative Boltzmann Inversion, but this error keeps me
dizzy.

Whenever I use -rdd options, it gives another error like domain
decomposition error with other options recommended. Whenever I use -nt
options, the simulation goes well but the simulation trajectory seem weird
that some molecules are going out the simulation box

It seems tricky to find what is the problem.

Thank you.

Best regards,
Changwoon Jang

On Tue, Aug 30, 2016 at 8:37 AM, Justin Lemkul  wrote:

>
>
> On 8/29/16 6:02 PM, Chang Woon Jang wrote:
>
>> Dear Gromacs Users,
>>
>>
>> I have a Fatal error as follow. The error says -rdd option or -ddcheck.
>> How
>> can I properly use these options? Is the following command the proper use
>> of these options?
>>
>> gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -rdd 1.5
>>>
>> -ddcheck
>>
>>
> Yes, but note that -ddcheck is on by default anyway, and you should look
> into why this might be happening.  You can get around this error, but it
> often indicates instability.  Without a complete description of what your
> system is, what you've previously done to prepare, minimize, equilibrate,
> etc. we're sort of just guessing here.  If the system is coarse grain, then
> use of a large -rdd is typical (as you will see from many threads in the
> archive that address this case specifically).
>
> -Justin
>
> Thank you.
>>
>>
>> 1 of the 1612 bonded interactions could not be calculated because some
>> atoms involved moved further apart than the multi-body cut-off distance
>> (1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for
>> pairs and tabulated bonds also see option -ddcheck
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>>
>>
>>
>>
>> Best regards,
>> Changwoon Jang,
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * 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.
>



-- 
Best regards,
Changwoon Jang,

Postdoctoral Research Fellow
Department of Chemical & Biological Engineering, Drexel University
3141 Chestnut Street, Philadelphia, PA 19104

Voice: (662) 617-2267
E-mail: cj...@drexel.edu
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Re: [gmx-users] Help with MD of water

[Dan Gil]

Hi,

There is a method in gromacs to insert water molecules into a box of size
defined by you. Depending on the version of gromacs you have, it will be
something like gmx insert-molecules.

Dan

On Tuesday, August 9, 2016, Omamuyovwi Akemu 
wrote:

> Dear Gromacs Users,
> I will like to do a molecular dynamics simulation of water in gromacs.
> Thereafter obtain thermodynamics observable like potential energy and well
> as structural and dynamics properties of the system.
>
> However, I kindly request for help with the topology file (.top) and
> molecular structure file (.gro) or a guide to kick off the simulation.
> I will really appreciate any comment.Thank you.
> Jolayemi Omamuyovwi RitaResearch Student,University of Benin,Nigeria.
> Sent from Yahoo Mail on Android
> --
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>
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>
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>
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Re: [gmx-users] evaluation of influence of pH on the stability of protein

[Justin Lemkul]

On 8/29/16 3:10 PM, Mahboobeh Eslami wrote:

 Hi all Gmx usersI want to evaluate influence of pH on the stability of  
protein.  can I use MD simulation for this goal? thanks



Protonate the protein and any other relevant species in different forms 
characteristic of the dominant form at each given pH.  The better way to do this 
is using constant-pH methods, such as those available in CHARMM.  I believe 
there are implementations of this in GROMACS, but they are not natively supported.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

[Justin Lemkul]

On 8/29/16 6:02 PM, Chang Woon Jang wrote:

Dear Gromacs Users,


I have a Fatal error as follow. The error says -rdd option or -ddcheck. How
can I properly use these options? Is the following command the proper use
of these options?


gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -rdd 1.5

-ddcheck



Yes, but note that -ddcheck is on by default anyway, and you should look into 
why this might be happening.  You can get around this error, but it often 
indicates instability.  Without a complete description of what your system is, 
what you've previously done to prepare, minimize, equilibrate, etc. we're sort 
of just guessing here.  If the system is coarse grain, then use of a large -rdd 
is typical (as you will see from many threads in the archive that address this 
case specifically).


-Justin


Thank you.


1 of the 1612 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.5 nm) or the two-body cut-off distance (1.5 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS




Best regards,
Changwoon Jang,



--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] x,y,z components of forces on each atom

[Justin Lemkul]

On 8/30/16 8:32 AM, Markus Kaukonen wrote:

Dear All,
I tried to get forces acting on every atom (fx, fy, fz, not the total force
on atom).
Is this somehow possible with standard gromacs 2016?


Extract them from the .trr file with gmx traj -of.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] minimum distance between the protein and its mirror image

[Justin Lemkul]

On 8/29/16 9:20 PM, OuyangYanhua wrote:

The minimum protein-image distance is less than the value 2.0nm, such as t 
around 1.6nm above. Does it mean my simulation is failed in the box size set?


Please read the first sentence of my previous reply.

-Justin


在 2016年8月29日，下午8:58，Justin Lemkul  写道：



On 8/29/16 5:02 AM, YanhuaOuyang wrote:

Hi,
  I am running a REMD of a disordered protein, I visualized the trajectory in 
VMD and I found that the protein is very close to the box edge.
  Then I use "gmx mindist " to  check  if a protein has seen its periodic image during 
simulation. When I used the command "gmx mindist -f remd_01.pdb -s remd.tpr -od mindist.xvg 
-pi" I choose the 1 group---protein. I choose some data from  mindist.xvg, they are as follow:
   02.800  5.225  7.200  7.200  7.200
   22.793  5.136  7.200  7.200  7.200
   42.804  5.002  7.200  7.200  7.200
   62.777  5.176  7.200  7.200  7.200
   82.820  5.187  7.200  7.200  7.200
   10   2.871  5.043  7.200  7.200  7.200
   12   2.788  5.089  7.200  7.200  7.200
   14   2.882  4.892  7.200  7.200  7.200
  
   5154 4.153  3.415  7.200  7.200  7.200
   5156 4.222  3.483  7.200  7.200  7.200
   5158 4.154  3.608  7.200  7.200  7.200
   5172 3.607  4.124  7.200  7.200  7.200
   5174 3.556  4.140  7.200  7.200  7.200
   5176 3.303  4.430  7.200  7.200  7.200
   5178 3.291  4.297  7.200  7.200  7.200
   ...
   5880 1.659  5.595  7.200  7.200  7.200
   5882 1.787  5.564  7.200  7.200  7.200
   5884 1.718  5.575  7.200  7.200  7.200
   5886 1.669  5.654  7.200  7.200  7.200
   5888 1.636  5.752  7.200  7.200  7.200
   5890 1.590  5.761  7.200  7.200  7.200
   5892 1.620  5.786  7.200  7.200  7.200
   5894 1.513  5.791  7.200  7.200  7.200
   5896 1.523  5.908  7.200  7.200  7.200
I set the short-range VDW and electrostatic cutoffs=1.0 nm, the distance 
between the outside of protein and the edge of box is 1.0 nm. the Minimum 
distance to periodic image ranges from 1.5 nm to 4.2 nm from the data above. 
While the deal value should be at least 2.0 nm, which is double the cutoff.
Do anyone knows the simulation is normal and if a protein has seen its periodic 
image during simulation?


It has not seen its periodic image with cutoffs = 1.0 nm.  You have a very thin 
shell of water around the protein, though, which means there could be some 
artificial ordering, but whether or not that's enough to seriously perturb the 
dynamics is not immediately clear.


which group should I choose when i using gmx mindist, protein, C-alpha or some 
else?



Protein.  You need to verify that all protein atoms behaved correctly.  CA 
atoms are unlikely to ever see their own periodic images unless you have done 
something horribly wrong in setting up your box.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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[gmx-users] x,y,z components of forces on each atom

[Markus Kaukonen]

Dear All,
I tried to get forces acting on every atom (fx, fy, fz, not the total force
on atom).
Is this somehow possible with standard gromacs 2016?
terveisin, Markus

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Re: [gmx-users] Odd behaviour of editconf or VMD?

[Quyen V. Vu]

> > Hi,
> > 
> >   I am trying to solvate a small DNA molecule. Since I don't want so
> > 
> > simulate more waters than what is really neccessary, I decided to try the
> > dodecahdron and octahedron unit cells.
> > 
> >   After I added waters I went to examine the resulting structures in VMD
> > 
> > only to find that the octahedron and dodecahedron cells are completely
> > wrong. Instead of the familiar shape (roughly a cube with trimmed edges
> > for
> > dodeachedron), I am greeted with a parallelepiped-like shape.
> > 
> >   I tried Gromacs 5.0.7, 5.1.3, 2016 but the results seem to be always the
> > 
> > same. Is this an expected behaviour? How do I "reconstitute" the resulting
> > structure?
> > 
> > Thanks,
> > Jernej
> > --
I read at somewhere that VMD hasn't support for dodecahedron box type yet and 
VMD will use a vector by the first three number for cubic dimension. 
Don't worry about that, your system still is dodecahedron
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[gmx-users] shear flow

[pari lotfi]

dear all

I want to simulate a box with two walls. One of them is fixed and other is
moving with steady velocity in a certain direction. I am going to produce a
shear flow.
If I constrain wall in two directions is enough? How can I produce fixed
velocity in other direction?

Thanks,
Pari
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[gmx-users] evaluation of influence of pH on the stability of protein

[Mahboobeh Eslami]

 On Monday, August 29, 2016 11:40 PM, Mahboobeh Eslami 
 wrote:
 

  Hi all Gmx usersI want to evaluate influence of pH on the stability of  
protein.  can I use MD simulation for this goal? thanks






   
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Re: [gmx-users] Odd behaviour of editconf or VMD?

[Tsjerk Wassenaar]

Hi Jernej,

This is simpler in two dimensions:
Consider a hexagonal unit cell.
Draw it, together with the surrounding copies (7 hexagons total).
Now connect the central hexagon with the right horizontal neighbor, and
with the 'northeast' neighbour.
Connect these two neighbors with their other common neighbor.
You drew a parallelogram.
Check that the contents of the parallelogram is the same as that of any
hexagon.
Now think of how it works with a rhombic dodecahedron and a parallelepiped.

Cheers,

Tsjerk


On Tue, Aug 30, 2016 at 10:17 AM, Jernej Zidar 
wrote:

> Hi,
>   I am trying to solvate a small DNA molecule. Since I don't want so
> simulate more waters than what is really neccessary, I decided to try the
> dodecahdron and octahedron unit cells.
>
>   After I added waters I went to examine the resulting structures in VMD
> only to find that the octahedron and dodecahedron cells are completely
> wrong. Instead of the familiar shape (roughly a cube with trimmed edges for
> dodeachedron), I am greeted with a parallelepiped-like shape.
>
>   I tried Gromacs 5.0.7, 5.1.3, 2016 but the results seem to be always the
> same. Is this an expected behaviour? How do I "reconstitute" the resulting
> structure?
>
> Thanks,
> Jernej
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>



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[gmx-users] Odd behaviour of editconf or VMD?

[Jernej Zidar]

Hi,
  I am trying to solvate a small DNA molecule. Since I don't want so
simulate more waters than what is really neccessary, I decided to try the
dodecahdron and octahedron unit cells.

  After I added waters I went to examine the resulting structures in VMD
only to find that the octahedron and dodecahedron cells are completely
wrong. Instead of the familiar shape (roughly a cube with trimmed edges for
dodeachedron), I am greeted with a parallelepiped-like shape.

  I tried Gromacs 5.0.7, 5.1.3, 2016 but the results seem to be always the
same. Is this an expected behaviour? How do I "reconstitute" the resulting
structure?

Thanks,
Jernej
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Re: [gmx-users] X Amino Acids for Building CG Structure

[Tsjerk Wassenaar]

Hi Elka,

Methyl asparagine is not known by DSSP and is not availble in Martini.
You're probably best off replacing it by asparagine:

sed '/^ATOM/s/MEN/ASN/' 1HG0.pdb > out.pdb

Cheers,

Tsjerk

On Fri, Aug 26, 2016 at 11:26 AM, Elka Firmanda  wrote:

> Hi, I just got "X" amino acids on DSSP, what does it means ? when I use the
> DSSP file to build coarse grained structure with martini 2.2 force field, I
> lost some amino acids because of this "x" amino acids on DSSP. So, how to
> build CG structure if I have this "x" amino acids ? I want to build CG
> structure for phycocyanin (1GH0) chain A-F. The "x" amino acids refers to
> modified residues called "MEN", L-Peptide Linking. Thank you for your help.
>
>
> *Elka Firmanda*
> Graduate Student
> Biophysics Division,
> ​ ​
> Department of Physics
> Faculty of Mathematics and Natural Sciences
> Bogor Agricultural University, Indonesia 16680
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Re: [gmx-users] QM/MM simulations (Mark Abraham)

[Groenhof, Gerrit]

Hi,

Unless there are no atoms in the QM region, the QM energy should not be zero. 

Can you confirm that mdrun writes an input file (input.com)? and gaussian is 
executed?

If not, has gromacs been compiled with QMMM support 
(GMX_QMMM_PROGRAM:STRING=gaussian)?

Best,

Gerrit


Hi,

Sadly, most of the QM/MM interfaces have been lacking a maintainer on the
GROMACS side for quite a number of years. You should definitely be
following http://wwwuser.gwdg.de/~ggroenh/qmmm.html closely.

Mark

On Mon, Aug 29, 2016 at 9:36 PM Clinton King 
wrote:

> I'm performing a QM/MM (using Gaussian 09 and Gromacs 5.1.2) simulation of
> a single molecule of octanol in a box of water. In examining the standard
> output, it appears that call to Gaussian is proceeding as expected, but
> looking at the log file, it doesn't appear that quantum energy is being
> communicated correctly, ie the output looks like the following:
>
>
>
>Step   Time Lambda
>70007.00.0
>
>Energies (kJ/mol)
> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>  Quantum En.
> 2.45033e+04   -1.74106e+02   -1.86935e+056.68753e+010.0e+00
>   Potential  Kinetic En. Total EnergyTemperature
>  Pres. DC (bar)
>-1.62539e+053.00966e+04   -1.32443e+052.97582e+02   -2.34549e+01
>  Pressure (bar)   Constr. rmsd
>-7.37300e+018.07450e-06
>
>
> Notice that the entry for Quantum En. is 0.000.
>
> Has anyone else seen this problem before? If so, what did you do about it?
>
> --
> Clinton King
> Graduate Student
> Chemistry Department
> Brigham Young University
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