[gmx-users] Re: MD Simulation regarding

[XAvier Periole]

Hi Rekkha,

you better off sending your post on the list to get comments from
more people.

If your are new in MD simulations and gromacs. The best for you is
to go through a couple of tutorials of protein simulations. I do not
know a links by heart but I am sure by searching the archive of
gromacs user-list or using google you'll find what you need.

Good luck,
XAvier.

On Aug 18, 2010, at 8:50 AM, rekkha nivethitha wrote:



Dear Sir,

Yesterday , i posted one query in gmx-users list: Such as,

"Hi frnds,

On running, Molecular dynamics simulation of protein-protein  
complex, While

running md run, i got this error,
*
"Back Off! I just backed up complex_pr1.trr to ./#complex_pr1.trr.5#

Back Off! I just backed up complex_pr1.edr to ./#complex_pr1.edr.5#


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.011042, max 4.472447 (between atoms 12 and 14)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.15#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.15#
- Show quoted text -

Wrote pdb files with previous and current coordinates

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.068209, max 23.054199 (between atoms 10 and 12)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
37 39   51.40.0589   0.1043  0.1360
37 38   46.00.0457   0.0811  0.1230
34 36   67.70.0255   0.1339  0.1530
34 35   69.40.0269   0.1376  0.1530
33 37   77.90.4780   0.1629  0.1530
33 34   97.40.4847   0.1141  0.1530
31 33  103.30.2087   0.4628  0.1470
31 32   63.00.1981   0.0359  0.1000
29 31   70.60.4388   0.2060  0.1330
29 30   54.50.2491   0.1016  0.1230
25 28  167.90.1444   0.0334  0.1530
25 26  140.50.1344   0.0404  0.1430
24 29  101.60.3497   0.2598  0.1530
24 25   42.70.2115   0.2662  0.1530
22 24   60.80.3511   0.2556  0.1470
22 23   91.30.1603   0.1401  0.1000
20 22   86.30.1443   1.1227  0.1330
20 21  134.20.1908   0.8440  0.1230
17 19  173.10.4358   1.5698  0.1530
17 18  173.50.4358   1.5704  0.1530
16 20  174.60.6605   2.0535  0.1530
16 17  177.40.3602   2.8668  0.1530
14 16  168.80.2643   2.9856  0.1470
14 15  166.10.3248   1.9914  0.1000
12 14  176.20.7278   3.1437  0.1330
12 13  177.00.3443   2.5072  0.1230
10 12  174.80.3544   3.6803  0.1530
10 11  169.20.4052   1.7864  0.1530
 8 10  173.10.5139   1.8491  0.1470
 8  9  151.40.0964   0.7325  0.1000
 6  8  115.10.0879   0.8155  0.1330
 6  7   53.80.1958   0.0677  0.1230
 4  5   56.90.1444   0.0413  0.1530

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.16#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.16#


Wrote pdb files with previous and current coordinates
starting mdrun 'Protein'
1 steps, 20.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.511037, max 177.073975 (between atoms 12 and 14)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
39 40  104.80.1585   0.1484  0.1000
37 39  147.00.0589   0.6971  0.1360
37 38  177.10.0457   0.6713  0.1230
34 36  158.30.0255   0.7496  0.1530
34 35  159.00.0269   0.7308  0.1530
33 37  162.20.4780   0.9895  0.1530
33 34  173.70.4847   0.9904  0.1530
31 33  115.70.2087   0.9548  0.1470
31 32  177.00.1981   0.3387  0.1000
29 31  128.40.4388   0.2813  0.1330
29 30  159.00.2491   0.2681  0.1230
24 29  105.70.3497   0.6145  0.1530
24 25  105.50.2115   0.3658  0.1530
22 24   90.50.3511   0.3786  0.1470
22 23   75.80.1603   0.1584  0.1000
20 22   85.70.1443   4.4331  0.1330
20 21  146.20.1908   4.6893  0.1230
17 19  172.30.4358  11.1229  0.1530
17 18  172.60.4358  11.1267  0.1530
16 20  172.60.6605  15.2461  0.1530
16 17  178.10.3602  20.4103  0.1530
14 16  173.50.2643  20.5192  0.1470
14 15  170.90.3248  14.1432  0.1000
12 14  174.80.7278  23.6838  0.1330
12 13  177.40.3443  18.2694  0.1230
10 12  175.80.3544  26.0403  0.1530
10 11  168.90.4052  13.2

[gmx-users] carbohydrate parameters in ffG53a6

[Jianhui Tian]

Hi,

I want to do some simulations about carbohydrates and glycolipid. In the
ffG53a6.rtp file, I just see limited parameters for carbohydrate, like
monosaccharide Glucose, Mannose and Galactose. What parameters can be used
for others like arabinose? Also, is there any parameters available in the
Gromacs force field for glycolipid?

Jianhui
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[gmx-users] reg QM/MM configuring error

[vidhya sankar]

Dear  gmxuser

when i try to configure mopac7-1.10 to interface with gromacs . it end in 
the following error 
../lib/cpp sanity check fails
is there is any suggestion to solve this problem ? it would be helpful to me 

thanks in advance i am expecting yours re


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Re: [gmx-users] Speeding up simulation

[Gaurav Goel]

Sapna,

Is there a particular reason you're using a box so much larger than the
droplet diameter? If your only concern is that periodic images should not
see each-other maybe you can use a box length=droplet diameter+2*largest
cut-off in the system.

Also using a more spherical box shape such as  rhombic dodecahedron or the
truncated octahedron will help you in reducing the volume of unfilled space.

-Gaurav

On Tue, Aug 17, 2010 at 5:40 PM, sapna sarupria wrote:

> Hi Justin
>
> Thanks for your input. I guess I will do some more literature search and
> try to optimize the simulations as much as I can.
>
> Thanks,
> Sapna
>
>
> On Tue, Aug 17, 2010 at 5:36 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> sapna sarupria wrote:
>>
>>> Hi Justin
>>> Thanks for your response. I suspect that it is the same thing. Is there a
>>> way to make gromacs use PME only within a certain region of the simulation
>>> box? Also, how does one know how to fix the load imbalances (in this
>>> context)?
>>>
>>
>> There is no way to limit PME to certain ranges.  It is a method for
>> solving infinite sums.  Usually PME is a poor choice for in vacuo
>> simulations and the like, since there's nothing to be done for most of the
>> simulation box.  You may want to see how others (in the literature) deal
>> with droplet-type simulations.
>>
>> -Justin
>>
>>
>>> Thanks for your help.
>>>
>>> Sapna
>>>
>>> On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote:
>>>
>>>
>>>
>>>sapna sarupria wrote:
>>>
>>>Hi all,
>>>
>>>I am running (NVT) simulations of a drop of water (~5 nm in
>>>radius) in a big box (~25 nm) in a box and find that the
>>>simulations are rather slow. I am getting about 0.8 ns per day
>>>when a simulation of bulk system of equivalent number of waters
>>>will be much faster. The number of waters is ~12000. I was
>>>wondering if anyone can suggest methods with which I can speed
>>>up the simulations. I am using domain decomposition and
>>>optimize_fft is set to yes. PME is used for the electrostatics.
>>>
>>>
>>>I would suspect that the lag comes from a lot of unused PME
>>>calculations. During your run, PME grid points will be assigned to
>>>vacuum space, for which nothing needs to be done.  You can check
>>>imbalances and performance loss in the log file.
>>>
>>>-Justin
>>>
>>>
>>>Thank you
>>>
>>>Sincerely
>>>Sapna
>>>
>>>
>>>-- 
>>>
>>>Justin A. Lemkul
>>>Ph.D. Candidate
>>>ICTAS Doctoral Scholar
>>>MILES-IGERT Trainee
>>>Department of Biochemistry
>>>Virginia Tech
>>>Blacksburg, VA
>>>jalemkul[at]vt.edu  | (540) 231-9080
>>>
>>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>>
>>>-- gmx-users mailing listgmx-users@gromacs.org
>>>
>>>
>>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>Please search the archive at http://www.gromacs.org/search before
>>>posting!
>>>Please don't post (un)subscribe requests to the list. Use the www
>>>interface or send it to gmx-users-requ...@gromacs.org
>>>.
>>>
>>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>
>>>
>>> --
>>> Sapna Sarupria
>>> Post-doctoral Researcher
>>> Princeton University
>>> New Jersey 08540
>>> U.S.A.
>>>
>>> Life isn't about finding yourself. Life is about creating yourself. --
>>> George Bernard Shaw.
>>> Dare to Dream
>>>
>>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
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>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
>
> --
> Sapna Sarupria
> Post-doctoral Researcher
> Princeton University
> New Jersey 08540
> U.S.A.
>
> Life isn't about finding yourself. Life is about creating yourself. --
> George Bernard Shaw.
> Dare to Dream
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Software to generate polymer coordinates

[Dallas Warren]

I have been searching for awhile now trying to find a script / software
package that will generate the coordinates of a polymer.  There are some
that will repeat a simple unit and there is an online one that will
allow you to generate some, but you can only use their predefined
monomers (http://wwmm-svc.ch.cam.ac.uk/polydemo/).

What I am after is something that you can specify your own monomer
units, how they link together, able to handle more than one monomer,
manner in which monomers are bonded (alternating, periodic, statistical,
block) and may be even grafts.

Has anyone found or know of one that can do anything like this?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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Re: [gmx-users] Speeding up simulation

[sapna sarupria]

Hi Justin

Thanks for your input. I guess I will do some more literature search and try
to optimize the simulations as much as I can.

Thanks,
Sapna

On Tue, Aug 17, 2010 at 5:36 PM, Justin A. Lemkul  wrote:

>
>
> sapna sarupria wrote:
>
>> Hi Justin
>> Thanks for your response. I suspect that it is the same thing. Is there a
>> way to make gromacs use PME only within a certain region of the simulation
>> box? Also, how does one know how to fix the load imbalances (in this
>> context)?
>>
>
> There is no way to limit PME to certain ranges.  It is a method for solving
> infinite sums.  Usually PME is a poor choice for in vacuo simulations and
> the like, since there's nothing to be done for most of the simulation box.
>  You may want to see how others (in the literature) deal with droplet-type
> simulations.
>
> -Justin
>
>
>> Thanks for your help.
>>
>> Sapna
>>
>> On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>sapna sarupria wrote:
>>
>>Hi all,
>>
>>I am running (NVT) simulations of a drop of water (~5 nm in
>>radius) in a big box (~25 nm) in a box and find that the
>>simulations are rather slow. I am getting about 0.8 ns per day
>>when a simulation of bulk system of equivalent number of waters
>>will be much faster. The number of waters is ~12000. I was
>>wondering if anyone can suggest methods with which I can speed
>>up the simulations. I am using domain decomposition and
>>optimize_fft is set to yes. PME is used for the electrostatics.
>>
>>
>>I would suspect that the lag comes from a lot of unused PME
>>calculations. During your run, PME grid points will be assigned to
>>vacuum space, for which nothing needs to be done.  You can check
>>imbalances and performance loss in the log file.
>>
>>-Justin
>>
>>
>>Thank you
>>
>>Sincerely
>>Sapna
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> --
>> Sapna Sarupria
>> Post-doctoral Researcher
>> Princeton University
>> New Jersey 08540
>> U.S.A.
>>
>> Life isn't about finding yourself. Life is about creating yourself. --
>> George Bernard Shaw.
>> Dare to Dream
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Sapna Sarupria
Post-doctoral Researcher
Princeton University
New Jersey 08540
U.S.A.

Life isn't about finding yourself. Life is about creating yourself. --
George Bernard Shaw.
Dare to Dream
-- 
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Re: [gmx-users] Speeding up simulation

[Justin A. Lemkul]

sapna sarupria wrote:

Hi Justin
Thanks for your response. I suspect that it is the same thing. Is there 
a way to make gromacs use PME only within a certain region of the 
simulation box? Also, how does one know how to fix the load imbalances 
(in this context)?


There is no way to limit PME to certain ranges.  It is a method for solving 
infinite sums.  Usually PME is a poor choice for in vacuo simulations and the 
like, since there's nothing to be done for most of the simulation box.  You may 
want to see how others (in the literature) deal with droplet-type simulations.


-Justin



Thanks for your help.

Sapna

On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul > wrote:




sapna sarupria wrote:

Hi all,

I am running (NVT) simulations of a drop of water (~5 nm in
radius) in a big box (~25 nm) in a box and find that the
simulations are rather slow. I am getting about 0.8 ns per day
when a simulation of bulk system of equivalent number of waters
will be much faster. The number of waters is ~12000. I was
wondering if anyone can suggest methods with which I can speed
up the simulations. I am using domain decomposition and
optimize_fft is set to yes. PME is used for the electrostatics.


I would suspect that the lag comes from a lot of unused PME
calculations. During your run, PME grid points will be assigned to
vacuum space, for which nothing needs to be done.  You can check
imbalances and performance loss in the log file.

-Justin


Thank you

Sincerely
Sapna


-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- 
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Please search the archive at http://www.gromacs.org/search before
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.
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--
Sapna Sarupria
Post-doctoral Researcher
Princeton University
New Jersey 08540
U.S.A.

Life isn't about finding yourself. Life is about creating yourself. -- 
George Bernard Shaw.

Dare to Dream



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] Speeding up simulation

[sapna sarupria]

Hi Justin
Thanks for your response. I suspect that it is the same thing. Is there a
way to make gromacs use PME only within a certain region of the simulation
box? Also, how does one know how to fix the load imbalances (in this
context)?

Thanks for your help.

Sapna

On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul  wrote:

>
>
> sapna sarupria wrote:
>
>> Hi all,
>>
>> I am running (NVT) simulations of a drop of water (~5 nm in radius) in a
>> big box (~25 nm) in a box and find that the simulations are rather slow. I
>> am getting about 0.8 ns per day when a simulation of bulk system of
>> equivalent number of waters will be much faster. The number of waters is
>> ~12000. I was wondering if anyone can suggest methods with which I can speed
>> up the simulations. I am using domain decomposition and optimize_fft is set
>> to yes. PME is used for the electrostatics.
>>
>
> I would suspect that the lag comes from a lot of unused PME calculations.
> During your run, PME grid points will be assigned to vacuum space, for which
> nothing needs to be done.  You can check imbalances and performance loss in
> the log file.
>
> -Justin
>
>
>> Thank you
>>
>> Sincerely
>> Sapna
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
Sapna Sarupria
Post-doctoral Researcher
Princeton University
New Jersey 08540
U.S.A.

Life isn't about finding yourself. Life is about creating yourself. --
George Bernard Shaw.
Dare to Dream
-- 
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Speeding up simulation

[Justin A. Lemkul]

sapna sarupria wrote:

Hi all,

I am running (NVT) simulations of a drop of water (~5 nm in radius) in a 
big box (~25 nm) in a box and find that the simulations are rather slow. 
I am getting about 0.8 ns per day when a simulation of bulk system of 
equivalent number of waters will be much faster. The number of waters is 
~12000. I was wondering if anyone can suggest methods with which I can 
speed up the simulations. I am using domain decomposition and 
optimize_fft is set to yes. PME is used for the electrostatics.


I would suspect that the lag comes from a lot of unused PME calculations. 
During your run, PME grid points will be assigned to vacuum space, for which 
nothing needs to be done.  You can check imbalances and performance loss in the 
log file.


-Justin



Thank you

Sincerely
Sapna



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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[gmx-users] Re: NPH Simulations

[sapna sarupria]

Hi all,

I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big
box (~25 nm) in a box and find that the simulations are rather slow. I am
getting about 0.8 ns per day when a simulation of bulk system of equivalent
number of waters will be much faster. The number of waters is ~12000. I was
wondering if anyone can suggest methods with which I can speed up the
simulations. I am using particle decomposition and optimize_fft is set to
yes. PME is used for the electrostatics. I currently use 16 processors for
the simulation.

Thank you for your help and suggestions.

Sincerely
Sapna
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[gmx-users] Speeding up simulation

[sapna sarupria]

Hi all,

I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big
box (~25 nm) in a box and find that the simulations are rather slow. I am
getting about 0.8 ns per day when a simulation of bulk system of equivalent
number of waters will be much faster. The number of waters is ~12000. I was
wondering if anyone can suggest methods with which I can speed up the
simulations. I am using domain decomposition and optimize_fft is set to yes.
PME is used for the electrostatics.

Thank you

Sincerely
Sapna
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Re: [gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff

[Mark Abraham]

- Original Message -
From: Alan 
Date: Tuesday, August 17, 2010 21:24
Subject: [gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff
To: Gromacs 

> Hi there,
> I've been looking at amber ff implementation of gmx 4.5 since I am familiar 
> to Sorin's ffamber works and I am the developer of ACPYPE.> 
> I noticed that proper dih are not converted to RB anymore (which's great for 
> understanding) and to accomplish that apparently 2 new funct were added to 
> the gmx code, namely 4 and 9.  > 
> Needless to say that I couldn't find anything about funct 4 and 9 in the 
> current gmx manual.

Type 9 was added to facilitate CHARMM's multiple proper dihedrals, in git 
commit a7c597c778351f by Erik, whose message was 

Added support for dihedraltype 9, which allows multiple terms for proper 
dihedrals.
By listing a dihedral with type 9, grompp will now scan the force field to 
see if there are
multiple terms on _adjacent_ lines listed in the dihedraltypes section, and 
in that case add them all.

A code snippet in src/kernel/toppush.c reads

if(ft == 9)
{
/* Previously, we have always overwritten parameters if e.g. a 
torsion
 with the same atomtypes occurs on multiple lines. However, 
CHARMM and
 some other force fields specify multiple dihedrals over some 
bonds,
 including cosines with multiplicity 6 and somethimes even 
higher.
 Thus, they cannot be represented with Ryckaert-Bellemans terms.
 To add support for these force fields, Dihedral type 9 is 
identical to
 normal proper dihedrals, but repeated entries are allowed.
 */
bAllowRepeat = TRUE;
ft = 1;
}
 
 
> I would appreciate more information about it. Among other things I would like 
> to know, e.g., what funct 4 would have different from funct 1, since in the 
> seminal work of Sorin, amber impr. dih are treated as prop. dih in gromacs.
>From src/gmxlib/{ifunc,bondfree}.c and src/kernel/{topdirs,toppush}.c it can 
>be seen that dihedraltypes 4 and 1 call the same evaluation function. Perhaps 
>Erik can confirm this.

src/gmxlib/ifunc.c did suggest to me that something is not quite right...

  def_bonded  ("PDIHS","Proper Dih.", 4, 3, 3,  eNR_PROPER, pdihs   
  ),
  def_bonded  ("RBDIHS",   "Ryckaert-Bell.",  4, 6, 6,  eNR_RB, rbdihs  
  ),
  def_bonded  ("FOURDIHS", "Fourier Dih.",4, 4, 4,  eNR_FOURDIH, rbdihs 
  ),
  def_bonded  ("IDIHS","Improper Dih.",   4, 2, 2,  eNR_IMPROPER,idihs  
  ),
  def_bonded  ("PIDIHS",   "Improper Dih.",   4, 3, 3,  eNR_PROPER, pdihs   
  ),
  
If PIDIHS is an improper dihedral with the functional form of a proper 
dihedral, should it not use eNR_IMPROPER?

Mark

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[gmx-users] Re: NaCl

[Vitaly Chaban]

If you simulate such zwitterion with integer charges, the interaction
energy will always be overstated due to electronic polarization, so
the partial volume will always be smaller than experimentalists say.
You may try any ab ibitio method to calculate interaction energy and
partial charges (MK, CHELPG...) and obtain more reasonable energy
values. Then fit them to get the potential of some form.


--
Dr. Vitaly Chaban



On Tue, Aug 17, 2010 at 5:02 PM,   wrote:
> Hello,
>
>    I want to actually determine the charge effect on partial molar volume. I
> tried using zwitterion glycine, but the partial molar volume that I obtained
> is fairly less than what it should be, so I thought it might be the charge
> effect of two oppositely charged termini, and to understand that better I
> just wanted to use a simple molecule with +ve and -ve charge.
>
>   For the charges, I thought I would put +1 on Na+ and -1 on Cl-. But I
> think I should probably try NaCl crystal like suggested.
>
> Thanks.
>
> -Nisha P
>
>
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RE: [gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff

[Berk Hess]

Hi,

Erik was too lazy to document this, I now added it to the manual.
Type 4 is identical to type 1, it is only there to distinguish improper from 
proper dihedrals.
Type 9 is identical to type 1, except that multiple entries in dihedraltypes 
will lead to
multiple functions on one dihedral.

Berk

From: alanwil...@gmail.com
Date: Tue, 17 Aug 2010 12:16:16 +0100
To: gmx-users@gromacs.org
Subject: [gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff

Hi there,
I've been looking at amber ff implementation of gmx 4.5 since I am familiar to 
Sorin's ffamber works and I am the developer of ACPYPE.
I noticed that proper dih are not converted to RB anymore (which's great for 
understanding) and to accomplish that apparently 2 new funct were added to the 
gmx code, namely 4 and 9.


Needless to say that I couldn't find anything about funct 4 and 9 in the 
current gmx manual.
I would appreciate more information about it. Among other things I would like 
to know, e.g., what funct 4 would have different from funct 1, since in the 
seminal work of Sorin, amber impr. dih are treated as prop. dih in gromacs.


Many thanks,
Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge. 
80 Tennis Court Road, Cambridge CB2 1GA, UK.


>>http://www.bio.cam.ac.uk/~awd28<<



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[gmx-users] Re: about error when configuring Moapc inerface version for gromacs

[Vitaly Chaban]

It looks like you caused problems assigning environmental variables.

You may also find this guide to be useful:
http://chaban.at.ua/publ/md/gromacs_mopac_interface/1-1-0-10


Vitaly





>                              when i try to configure mopac7-1.10 to interface 
> with gromacs . it end in
> the following error
> ../lib/cpp sanity check fails
> is there is any suggestion to solve this problem ? it  would be helpful to me
>
> thanks in advance i am expecting yours rep
>
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Re: [gmx-users] about erron when configuring Moapc inerface version for gromacs

[Mark Abraham]

- Original Message -
From: vidhya sankar 
Date: Tuesday, August 17, 2010 21:48
Subject: [gmx-users] about erron when configuring Moapc inerface version for 
gromacs
To: gmx-users@gromacs.org

---
| > Dear Abragham sir
> 
>   when i try to configure mopac7-1.10 to 
> interface with gromacs . it end in 
> the following error 
> ../lib/cpp sanity check fails
> is there is any suggestion to solve this problem ? it  would be helpful to me 

Sounds like something is broken on your system - like no compiler is installed. 
Google "cpp sanity check"

Mark
 |
---

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Re: [gmx-users] "MD simulation of protein-protein complex"

[XAvier Periole]

That means that in your starting conformation you have strong forces
probably coming from back contacts.

minimization/equilibration should help removing them.

On Aug 17, 2010, at 12:29 PM, rekkha nivethitha wrote:


Hi frnds,

On running, Molecular dynamics simulation of protein-protein  
complex, While running md run, i got this error,


"Back Off! I just backed up complex_pr1.trr to ./#complex_pr1.trr.5#

Back Off! I just backed up complex_pr1.edr to ./#complex_pr1.edr.5#


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.011042, max 4.472447 (between atoms 12 and 14)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.15#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.15#
- Show quoted text -

Wrote pdb files with previous and current coordinates

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.068209, max 23.054199 (between atoms 10 and 12)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 37 39   51.40.0589   0.1043  0.1360
 37 38   46.00.0457   0.0811  0.1230
 34 36   67.70.0255   0.1339  0.1530
 34 35   69.40.0269   0.1376  0.1530
 33 37   77.90.4780   0.1629  0.1530
 33 34   97.40.4847   0.1141  0.1530
 31 33  103.30.2087   0.4628  0.1470
 31 32   63.00.1981   0.0359  0.1000
 29 31   70.60.4388   0.2060  0.1330
 29 30   54.50.2491   0.1016  0.1230
 25 28  167.90.1444   0.0334  0.1530
 25 26  140.50.1344   0.0404  0.1430
 24 29  101.60.3497   0.2598  0.1530
 24 25   42.70.2115   0.2662  0.1530
 22 24   60.80.3511   0.2556  0.1470
 22 23   91.30.1603   0.1401  0.1000
 20 22   86.30.1443   1.1227  0.1330
 20 21  134.20.1908   0.8440  0.1230
 17 19  173.10.4358   1.5698  0.1530
 17 18  173.50.4358   1.5704  0.1530
 16 20  174.60.6605   2.0535  0.1530
 16 17  177.40.3602   2.8668  0.1530
 14 16  168.80.2643   2.9856  0.1470
 14 15  166.10.3248   1.9914  0.1000
 12 14  176.20.7278   3.1437  0.1330
 12 13  177.00.3443   2.5072  0.1230
 10 12  174.80.3544   3.6803  0.1530
 10 11  169.20.4052   1.7864  0.1530
  8 10  173.10.5139   1.8491  0.1470
  8  9  151.40.0964   0.7325  0.1000
  6  8  115.10.0879   0.8155  0.1330
  6  7   53.80.1958   0.0677  0.1230
  4  5   56.90.1444   0.0413  0.1530

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.16#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.16#


Wrote pdb files with previous and current coordinates
starting mdrun 'Protein'
1 steps, 20.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.511037, max 177.073975 (between atoms 12 and 14)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 39 40  104.80.1585   0.1484  0.1000
 37 39  147.00.0589   0.6971  0.1360
 37 38  177.10.0457   0.6713  0.1230
 34 36  158.30.0255   0.7496  0.1530
 34 35  159.00.0269   0.7308  0.1530
 33 37  162.20.4780   0.9895  0.1530
 33 34  173.70.4847   0.9904  0.1530
 31 33  115.70.2087   0.9548  0.1470
 31 32  177.00.1981   0.3387  0.1000
 29 31  128.40.4388   0.2813  0.1330
 29 30  159.00.2491   0.2681  0.1230
 24 29  105.70.3497   0.6145  0.1530
 24 25  105.50.2115   0.3658  0.1530
 22 24   90.50.3511   0.3786  0.1470
 22 23   75.80.1603   0.1584  0.1000
 20 22   85.70.1443   4.4331  0.1330
 20 21  146.20.1908   4.6893  0.1230
 17 19  172.30.4358  11.1229  0.1530
 17 18  172.60.4358  11.1267  0.1530
 16 20  172.60.6605  15.2461  0.1530
 16 17  178.10.3602  20.4103  0.1530
 14 16  173.50.2643  20.5192  0.1470
 14 15  170.90.3248  14.1432  0.1000
 12 14  174.80.7278  23.6838  0.1330
 12 13  177.40.3443  18.2694  0.1230
 10 12  175.80.3544  26.0403  0.1530
 10 11  168.90.4052  13.2549  0.1530
  8 10  174.10.5139  13.7575  0.1470
  8  9  163.80.0964   4.7575  0.1000
  6  8  125.80.0879   4.2261  0.1330
  6  7  148.20.1958   0.9645  0.123

[gmx-users] about erron when configuring Moapc inerface version for gromacs

[vidhya sankar]

Dear Abragham sir

  when i try to configure mopac7-1.10 to interface 
with gromacs . it end in 
the following error 
../lib/cpp sanity check fails
is there is any suggestion to solve this problem ? it  would be helpful to me 

thanks in advance i am expecting yours rep


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[gmx-users] dihedraltypes funct 4 and 9 in gmx 4.5 amber ff

[Alan]

Hi there,

I've been looking at amber ff implementation of gmx 4.5 since I am familiar
to Sorin's ffamber works and I am the developer of ACPYPE.

I noticed that proper dih are not converted to RB anymore (which's great for
understanding) and to accomplish that apparently 2 new funct were added to
the gmx code, namely 4 and 9.

Needless to say that I couldn't find anything about funct 4 and 9 in the
current gmx manual.

I would appreciate more information about it. Among other things I would
like to know, e.g., what funct 4 would have different from funct 1, since in
the seminal work of Sorin, amber impr. dih are treated as prop. dih in
gromacs.

Many thanks,

Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Re: [gmx-users] Essential Dynamics

[Mark Abraham]

- Original Message -
From: pawan raghav 
Date: Tuesday, August 17, 2010 20:14
Subject: [gmx-users] Essential Dynamics
To: gmx-users@gromacs.org

> Dear Tsjerk, >   > It will be helpful to me if you would like to solve my 
> problem I have already read your tutorial and so many papers but I am really 
> confused and thats why mail to you. So please answer me which will help me 
> lot to understand right concept.

Tsjerk has already suggested gently that he's not going to teach you in this 
forum. People here do not have the time and resources for extensive one-on-one 
assistance - they're all volunteers sharing their wisdom that was earned with 
hard work. His tutorial material is a good bridge from abstract PCA to the 
kinds of PCA used in analysis molecular simulations. However if you do not 
understand what the covariance matrix contains or what its dimensions should 
be, then you will struggle to use the tools effectively.

Please follow his advice and search for suitable teaching material. There's no 
substitute for sound background knowledge in generating results in which you 
and others can have confidence. Perhaps 
http://en.wikipedia.org/wiki/Principal_component_analysis is a good start, or 
even a beginner-level linear algebra or multivariate statistics text suitable 
for a first-year university student. A university library should have several 
such.

Mark
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[gmx-users] "MD simulation of protein-protein complex"

[rekkha nivethitha]

*Hi frnds,

On running, Molecular dynamics simulation of protein-protein complex, While
running md run, i got this error,
*
"Back Off! I just backed up complex_pr1.trr to ./#complex_pr1.trr.5#

Back Off! I just backed up complex_pr1.edr to ./#complex_pr1.edr.5#


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.011042, max 4.472447 (between atoms 12 and 14)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.15#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.15#
- Show quoted text -

Wrote pdb files with previous and current coordinates

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.068209, max 23.054199 (between atoms 10 and 12)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 37 39   51.40.0589   0.1043  0.1360
 37 38   46.00.0457   0.0811  0.1230
 34 36   67.70.0255   0.1339  0.1530
 34 35   69.40.0269   0.1376  0.1530
 33 37   77.90.4780   0.1629  0.1530
 33 34   97.40.4847   0.1141  0.1530
 31 33  103.30.2087   0.4628  0.1470
 31 32   63.00.1981   0.0359  0.1000
 29 31   70.60.4388   0.2060  0.1330
 29 30   54.50.2491   0.1016  0.1230
 25 28  167.90.1444   0.0334  0.1530
 25 26  140.50.1344   0.0404  0.1430
 24 29  101.60.3497   0.2598  0.1530
 24 25   42.70.2115   0.2662  0.1530
 22 24   60.80.3511   0.2556  0.1470
 22 23   91.30.1603   0.1401  0.1000
 20 22   86.30.1443   1.1227  0.1330
 20 21  134.20.1908   0.8440  0.1230
 17 19  173.10.4358   1.5698  0.1530
 17 18  173.50.4358   1.5704  0.1530
 16 20  174.60.6605   2.0535  0.1530
 16 17  177.40.3602   2.8668  0.1530
 14 16  168.80.2643   2.9856  0.1470
 14 15  166.10.3248   1.9914  0.1000
 12 14  176.20.7278   3.1437  0.1330
 12 13  177.00.3443   2.5072  0.1230
 10 12  174.80.3544   3.6803  0.1530
 10 11  169.20.4052   1.7864  0.1530
  8 10  173.10.5139   1.8491  0.1470
  8  9  151.40.0964   0.7325  0.1000
  6  8  115.10.0879   0.8155  0.1330
  6  7   53.80.1958   0.0677  0.1230
  4  5   56.90.1444   0.0413  0.1530

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.16#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.16#


Wrote pdb files with previous and current coordinates
starting mdrun 'Protein'
1 steps, 20.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.511037, max 177.073975 (between atoms 12 and 14)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 39 40  104.80.1585   0.1484  0.1000
 37 39  147.00.0589   0.6971  0.1360
 37 38  177.10.0457   0.6713  0.1230
 34 36  158.30.0255   0.7496  0.1530
 34 35  159.00.0269   0.7308  0.1530
 33 37  162.20.4780   0.9895  0.1530
 33 34  173.70.4847   0.9904  0.1530
 31 33  115.70.2087   0.9548  0.1470
 31 32  177.00.1981   0.3387  0.1000
 29 31  128.40.4388   0.2813  0.1330
 29 30  159.00.2491   0.2681  0.1230
 24 29  105.70.3497   0.6145  0.1530
 24 25  105.50.2115   0.3658  0.1530
 22 24   90.50.3511   0.3786  0.1470
 22 23   75.80.1603   0.1584  0.1000
 20 22   85.70.1443   4.4331  0.1330
 20 21  146.20.1908   4.6893  0.1230
 17 19  172.30.4358  11.1229  0.1530
 17 18  172.60.4358  11.1267  0.1530
 16 20  172.60.6605  15.2461  0.1530
 16 17  178.10.3602  20.4103  0.1530
 14 16  173.50.2643  20.5192  0.1470
 14 15  170.90.3248  14.1432  0.1000
 12 14  174.80.7278  23.6838  0.1330
 12 13  177.40.3443  18.2694  0.1230
 10 12  175.80.3544  26.0403  0.1530
 10 11  168.90.4052  13.2549  0.1530
  8 10  174.10.5139  13.7575  0.1470
  8  9  163.80.0964   4.7575  0.1000
  6  8  125.80.0879   4.2261  0.1330
  6  7  148.20.1958   0.9645  0.1230
  4  6  149.40.2692   0.7665  0.1530
 129611 129612   90.00.1360   0.2674  0.1360
 129612 129613   90.00.1000   0.1416  0.1000

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.17#

[gmx-users] Essential Dynamics

[pawan raghav]

Dear Tsjerk,

It will be helpful to me if you would like to solve my problem I have
already read your tutorial and so many papers but I am really confused and
thats why mail to you. So please answer me which will help me lot to
understand right concept.

-- 
Pawan
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Re: [gmx-users] essential dynamics

[Tsjerk Wassenaar]

Hi Pawan,

This goes beyond a few lines of explanation. Move away from the tools
g_covar and g_anaeig slowly ;) and do some more background reading on
principal component analysis. I've tried to explain it in my tutorial
at http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html (which
will probably answer your questions) and there are many documents on
the internet describing PCA as a statistical tool.

Cheers,

Tsjerk

On Tue, Aug 17, 2010 at 9:56 AM, pawan raghav  wrote:
> Hi all,
>
> I have a confusion regarding "Essential Dynamics". I have read so many
> papers regarding PCA and ED most of the papers among them explained
> eigenvectors and eigenvalues are as follows:
>
> if a protein has 207 C alpha residues then the total no of eigenvectors are
> 3N X 3N, where N= no. of atoms i.e. 3 X 207 = 621 eigenvectors. is it means
> that an eigenvector represents an C-alpha residue?
>
> But manual described that representations the direction of motions.
>
> But 3N X 3N is a covariance matrix that means this represents 621 X 621
> eigenvectors is it true?
>
> Then when we plot a 2dproj.xvg file between eigenvector 1 and eigenvector 2,
> is it mean to plot a 2d graph between first two C-alpha atoms or first two
> structures?
>
> Please clearify me where I was wrong.
>
> The 2d graph shows oval and random large trajectory graph which represents
> the independent and dependent motion, may I know what does it mean?
>
> --
> Pawan
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands
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[gmx-users] Re: NaCl

[Vitaly Chaban]

Dear Nisha P.:

The bond parameters can be easily derived from any ab initio
calculation you like, although this will not remove the issue that
such system is fantastic. By the way, what charges do you suppose to
put on the counterions of your crazy molecule?

What is your reseach task in fact?

Good luck.
Dr. Vitaly Chaban

P.S. The Moore's Law will not continue to hold. :-)




>     I want to simulate a simple NaCl ion in water. I know the method
> using genion which adds individual Na+ and Cl- ion, but I wish to
> simulate Na-Cl connected rather than free ions floating in water. When
> I ran the grompp command I got the error:
> No default Bond types
> So I am thinking, I need to add b0 and Kb values for NaCl? Is that correct?
>
> I would really appreciate some help!
>
> Thanks.
>
> -Nisha P
>
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[gmx-users] essential dynamics

[pawan raghav]

Hi all,

I have a confusion regarding "Essential Dynamics". I have read so many
papers regarding PCA and ED most of the papers among them explained
eigenvectors and eigenvalues are as follows:

if a protein has 207 C alpha residues then the total no of eigenvectors are
3N X 3N, where N= no. of atoms i.e. 3 X 207 = 621 eigenvectors. is it means
that an eigenvector represents an C-alpha residue?

But manual described that representations the direction of motions.

But 3N X 3N is a covariance matrix that means this represents 621 X 621
eigenvectors is it true?

Then when we plot a 2dproj.xvg file between eigenvector 1 and eigenvector 2,
is it mean to plot a 2d graph between first two C-alpha atoms or first two
structures?

Please clearify me where I was wrong.

The 2d graph shows oval and random large trajectory graph which represents
the independent and dependent motion, may I know what does it mean?


-- 
Pawan
-- 
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