RE: [gmx-users] Hard Spheres

[Berk Hess]

> Subject: Re: [gmx-users] Hard Spheres
> From: sascha.hem...@bci.tu-dortmund.de
> To: gmx-users@gromacs.org
> Date: Thu, 9 Dec 2010 08:56:54 +0100
> 
> > On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel
> >  wrote:
> > Hi all!
> > 
> > I am trying to add some hard spheres to my simulation. As far
> > as i can
> > tell from the manual Gromacs supports only LJ or Buckingham
> > for
> > non-bonded interaction.
> > 
> > 
> > Why cant you use  LJ? By setting the attractive part equal to zero.
> >  
> The LJ Equation is 4 * eps * ( (sig/r)**12 - (sig/r)**6).
> If I either set sigma or epsilon to zero the Potential will become zero
> for all r

Search in the manual for combination rule 1, then you can set C6 and C12.
Also I just replied a week ago to a mail where a user wanted to set C6
to zero while supplying sigma and epsilon, you can do that by putting
a minus sign in front of the sigma.

Another option is using tabulated potentials (user), then you can use anything,
except for completely hard spheres, which would lead to infinite forces.

Berk

> > 
> > Is there a way to add hard spheres to lets say a simulation of
> > Water
> > molecules without interfering into the regular water-water
> > interaction?
> > 
> > Thanks a lot in advance,
> > 
> > Sascha
> > 
> > TU Dortmund
> > Laboratory of Thermodynamics
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
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> > posting!
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> > 
> 
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[gmx-users] water-air interface surface tension

[gromacs]

Hi, experts,
 
I'd like to calculate the surface tension at water-air interface using Gromacs.
which ensemble should i choose?
 when i run simulation, .mdp how can i select p-coupling?
 
whether should i use p-coupling?
 
I can creat a air-water-air structure (.gro)
 
Thanks?-- 
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Re: [gmx-users] water-air interface surface tension

[David van der Spoel]

On 2010-12-09 09.20, gromacs wrote:

Hi, experts,
I'd like to calculate the surface tension at water-air interface using
Gromacs.
which ensemble should i choose?
when i run simulation, .mdp how can i select p-coupling?
whether should i use p-coupling?

what do you think will happen when you use P coupling?

You may have a look in in
http://pubs.acs.org/cgi-bin/download.pl?la053284f/X8nx


I can creat a air-water-air structure (.gro)
Thanks?



163/126??iphone ipad





--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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RE: [gmx-users] Hard Spheres

[Sascha Hempel]

On Thu, 2010-12-09 at 09:11 +0100, Berk Hess wrote:
> 
> 
> > Subject: Re: [gmx-users] Hard Spheres
> > From: sascha.hem...@bci.tu-dortmund.de
> > To: gmx-users@gromacs.org
> > Date: Thu, 9 Dec 2010 08:56:54 +0100
> > 
> > > On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel
> > >  wrote:
> > > Hi all!
> > > 
> > > I am trying to add some hard spheres to my simulation. As far
> > > as i can
> > > tell from the manual Gromacs supports only LJ or Buckingham
> > > for
> > > non-bonded interaction.
> > > 
> > > 
> > > Why cant you use LJ? By setting the attractive part equal to zero.
> > > 
> > The LJ Equation is 4 * eps * ( (sig/r)**12 - (sig/r)**6).
> > If I either set sigma or epsilon to zero the Potential will become
> zero
> > for all r
> 
> Search in the manual for combination rule 1, then you can set C6 and
> C12.
> Also I just replied a week ago to a mail where a user wanted to set C6
> to zero while supplying sigma and epsilon, you can do that by putting
> a minus sign in front of the sigma.
> 
> Another option is using tabulated potentials (user), then you can use
> anything,
> except for completely hard spheres, which would lead to infinite
> forces.
> 
> Berk
> 

Thanks for your advice. I looked this up in the manual and experimented
a little with the functions. 
I can not just set C6 to 0 beacause then i will keep a repulsing
potential at long distances which will skrew with my system.
I could use a shift or switch function to take care of that, but since i
want some regular water in my system too this is not an option. 

So I am going to go with tabulated potentials. 
How "soft" do my hard spheres have to be to not cause any trouble for
the gromacs engine?

Sascha



> > > 
> > > Is there a way to add hard spheres to lets say a simulation of
> > > Water
> > > molecules without interfering into the regular water-water
> > > interaction?
> > > 
> > > Thanks a lot in advance,
> > > 
> > > Sascha
> > > 
> > > TU Dortmund
> > > Laboratory of Thermodynamics
> > > --
> > > gmx-users mailing list gmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
> > > 
> > 
> > -- 
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[gmx-users] Can the g_order calculate order parameters for two polymer backbone atoms?

[英雄不再寂寞]

Dear gmxers,
   I am planning to analyze order parameter using g_order, but some problems 
always puzzle me. For convenience, I describe the first problem as follows:
   Assume that there are two polymer chains H-[CH2-CH(OH)]n-H, now I want to 
calculate the order parameter of two carbon atoms in the monomer along the 
z-direction, that is, the Sz=1.5*-0.5, where θ is the angle between 
the z-axis of the simulation box and the vector from one carbon atom to another 
carbon atom. I have read the manual, only to find it seems that g_order has 
different aim designed for acyl chains with long carbon tails. In fact, I am 
not sure how it works from the manual. I wonder if the g_order can also 
calculate order parameters defined above for two polymer backbone atom. If it 
can, how to do it? Please kindly give me some hints. Thanks a lot for any reply.
  
 Yours sincerely,
 Chaofu Wu, Dr.-- 
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Re: [gmx-users] water-air interface surface tension

[vinothkumar mohanakrishnan]

Hi David

Can you tell me which journal, volume and page number. I am not able to
acess the link you have given. any help is highly appreciated

Regards
Vinoth

2010/12/9 David van der Spoel 

> On 2010-12-09 09.20, gromacs wrote:
>
>> Hi, experts,
>> I'd like to calculate the surface tension at water-air interface using
>> Gromacs.
>> which ensemble should i choose?
>> when i run simulation, .mdp how can i select p-coupling?
>> whether should i use p-coupling?
>>
> what do you think will happen when you use P coupling?
>
> You may have a look in in
> http://pubs.acs.org/cgi-bin/download.pl?la053284f/X8nx
>
>  I can creat a air-water-air structure (.gro)
>> Thanks?
>>
>>
>> 
>> 网易163/126邮箱百分百兼容iphone ipad邮件收发
>> 
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>
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[gmx-users] Pull simulation odditites when viewed in VMD

[Natalie Stephenson]

Hey,

I've been performing a pull simulation of a protein, all seems to work fine 
however after I convert the .xtc file into seperate .gro files and load those 
into VMD to visualise the simulation something weird happens.  Every 50 frames 
or so a random bond within the backbone of the protein (not necessarily near 
the point of pulling or unfolding) seems to extend and spike out massively from 
the structure - does anyone know why that would be happening?

Thanks for your help
Natalie


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Re: [gmx-users] Pull simulation odditites when viewed in VMD

[Justin A. Lemkul]

Natalie Stephenson wrote:

Hey,

I've been performing a pull simulation of a protein, all seems to work 
fine however after I convert the .xtc file into seperate .gro files and 
load those into VMD to visualise the simulation something weird 
happens.  Every 50 frames or so a random bond within the backbone of the 
protein (not necessarily near the point of pulling or unfolding) seems 
to extend and spike out massively from the structure - does anyone know 
why that would be happening? 



Please see FAQ #9:

http://www.gromacs.org/Documentation/FAQs

-Justin


Thanks for your help
Natalie




--


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] Hard Spheres

[devicerandom]

On 09/12/10 09:51, Sascha Hempel wrote:


Thanks for your advice. I looked this up in the manual and experimented
a little with the functions.
I can not just set C6 to 0 beacause then i will keep a repulsing
potential at long distances which will skrew with my system.
I could use a shift or switch function to take care of that, but since i
want some regular water in my system too this is not an option.

So I am going to go with tabulated potentials.
How "soft" do my hard spheres have to be to not cause any trouble for
the gromacs engine?


Test different function shapes -it's not easy, and also it depends on 
your temperature and desired time step. The smaller the time step, the 
steeper/hotter you can go, but of course at the price of slower 
simulations. I had the same issue and I used a combination of Morse 
potentials, a rigid one for the repulsive part and a softer one for the 
attractive basin (I need one as well, you maybe don't).


m.





Is there a way to add hard spheres to lets say a simulation of
Water
molecules without interfering into the regular water-water
interaction?

Thanks a lot in advance,

Sascha

TU Dortmund
Laboratory of Thermodynamics
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[gmx-users] crashed run

[shiva birgani]

Dear friends
Thanks for help
I did what you said. but now I have another question.
why when I compute RMSD, there is a turbulence in the digits  between two MD
runs (MD1 & MD2)?
Along 10nS RMSD values increase but after that in continued MD RMSD values
start with lower digits. So the obtained RMSD plot has turbulence in the gap
between two MD.
how can I solve this problem?
to clear this question I put the RMSD values of some frames below:

   0.0000.2210472
   0.0100.2029170
   0.0200.2312521
   0.0300.2153534
   0.0400.2236744
   0.0500.2186773
   0.0600.2058581
   0.0700.2236195
   0.0800.2124665
   0.0900.1984987
   0.1000.2133160
   0.1100.2032684
   0.1200.2185176
   0.1300.2375279
   0.1400.2209899
   0.1500.2517494
   0.1600.2250047
   0.1700.2311087
   0.1800.2404595
   0.1900.2289306
   0.2000.2239618
   .
   .
   .
   5.0000.1890597
   5.0120.1890515
   5.0250.2006893
   5.0320.1972803
   5.0440.1982047
   5.0520.1675302
   5.0640.1850004
   5.0720.1860897
   5.0840.2052469
   5.0920.1921552
   5.1040.2011560
   5.1110.1885858
   5.1240.2002560
   5.1310.1740426
   5.1430.1723358
   5.1560.1674020
   5.1680.1726498
   5.1760.1708745
   5.1880.1729662
   5.1950.1796937
   5.2080.1865102
   .
   .
   9.0000.1759290
   9.0120.1719585
   9.0250.1677127
   9.0370.1568936
   9.0400.1683941
   9.0520.1726477
   9.0640.1535644
   9.0760.1613303
   9.0890.1731772
   9.0920.1845323
   9.1040.1906714
   9.1160.1809433
   9.1280.1692949
   9.1310.1600803
   9.1430.1660035
   9.1560.1754447
   9.1680.1643370
   9.1710.1781539
   9.1830.1826023
   9.1950.1772111
   9.2080.1583686
   .
   .
  10.0000.0005027 ---here MD1 crashed and new
MD2 started
  10.0120.0855930
  10.0250.0906140
  10.0370.1090365
  10.0490.1284636
  10.0520.1079870
  10.0640.1182096
  10.0760.1337083
  10.0890.1404199
  10.0920.1518639
  10.1040.1318038
  10.1160.1288120
  10.1280.1413255
  10.1310.1318252
  10.1430.1459130
  10.1560.1559724
  10.1680.1299423
  10.1710.1178040
  10.1830.1542594
  10.1950.1464352
  10.2080.1217079
  .
  .
  15.0190.3443058
  15.01000210.3503898
  15.02000140.3517708
  15.03000160.3573279
  15.04000190.3375081
  15.05000210.3556643
  15.06000140.3347272
  15.07000160.3550032
  15.08000180.3570938
  15.09000210.3791857
  15.1130.3838716
  15.11000160.3931288
  15.12000180.3871831
  15.13000200.3749425
  15.14000130.3714155
  15.15000150.3525784
  15.16000180.3199620
  15.17000200.3337676
  15.18000130.3514860
  15.19000150.3480204
  15.2170.3494628
  .
  .
  20.0000.3118807
  20.0120.3075790
  20.0250.3048350
  20.0370.3090370
  20.0490.3213491
  20.05000110.3106411
  20.06000140.2958525
  20.07000160.2954315
  20.08000180.2988622
  20.0920.2828163
  20.1040.3012785
  20.1160.2912732
  20.1280.3035305
  20.13000110.3047263
  20.14000130.2943486
  20.15000150.2992145
  20.16000180.3017998
  20.1710.3055096
  20.1830.3006694
  20.1950.2961275
  20.2080.2953818
  .
  .
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Re: [gmx-users] crashed run

[Justin A. Lemkul]

shiva birgani wrote:


Dear friends
Thanks for help
I did what you said. but now I have another question.
why when I compute RMSD, there is a turbulence in the digits  between 
two MD runs (MD1 & MD2)?
Along 10nS RMSD values increase but after that in continued MD RMSD 
values start with lower digits. So the obtained RMSD plot has turbulence 
in the gap between two MD.

how can I solve this problem?


Please provide the exact commands you used to continue your run and carry out 
your RMSD analysis.  Without that precise information, the best guess is "you 
did something wrong."


You probably used the wrong .tpr file as your reference structure.  It seems odd 
to me that your t=0 RMSD is so high.


-Justin


to clear this question I put the RMSD values of some frames below:
  
   0.0000.2210472

   0.0100.2029170
   0.0200.2312521
   0.0300.2153534
   0.0400.2236744
   0.0500.2186773
   0.0600.2058581
   0.0700.2236195
   0.0800.2124665
   0.0900.1984987
   0.1000.2133160
   0.1100.2032684
   0.1200.2185176
   0.1300.2375279
   0.1400.2209899
   0.1500.2517494
   0.1600.2250047
   0.1700.2311087
   0.1800.2404595
   0.1900.2289306
   0.2000.2239618
   .
   .
   .
   5.0000.1890597
   5.0120.1890515
   5.0250.2006893
   5.0320.1972803
   5.0440.1982047
   5.0520.1675302
   5.0640.1850004
   5.0720.1860897
   5.0840.2052469
   5.0920.1921552
   5.1040.2011560
   5.1110.1885858
   5.1240.2002560
   5.1310.1740426
   5.1430.1723358
   5.1560.1674020
   5.1680.1726498
   5.1760.1708745
   5.1880.1729662
   5.1950.1796937
   5.2080.1865102
   .
   .
   9.0000.1759290
   9.0120.1719585
   9.0250.1677127
   9.0370.1568936
   9.0400.1683941
   9.0520.1726477
   9.0640.1535644
   9.0760.1613303
   9.0890.1731772
   9.0920.1845323
   9.1040.1906714
   9.1160.1809433
   9.1280.1692949
   9.1310.1600803
   9.1430.1660035
   9.1560.1754447
   9.1680.1643370
   9.1710.1781539
   9.1830.1826023
   9.1950.1772111
   9.2080.1583686
   .
   .
  10.0000.0005027 ---here MD1 crashed and 
new MD2 started

  10.0120.0855930
  10.0250.0906140
  10.0370.1090365
  10.0490.1284636
  10.0520.1079870
  10.0640.1182096
  10.0760.1337083
  10.0890.1404199
  10.0920.1518639
  10.1040.1318038
  10.1160.1288120
  10.1280.1413255
  10.1310.1318252
  10.1430.1459130
  10.1560.1559724
  10.1680.1299423
  10.1710.1178040
  10.1830.1542594
  10.1950.1464352
  10.2080.1217079
  .
  .
  15.0190.3443058
  15.01000210.3503898
  15.02000140.3517708
  15.03000160.3573279
  15.04000190.3375081
  15.05000210.3556643
  15.06000140.3347272
  15.07000160.3550032
  15.08000180.3570938
  15.09000210.3791857
  15.1130.3838716
  15.11000160.3931288
  15.12000180.3871831
  15.13000200.3749425
  15.14000130.3714155
  15.15000150.3525784
  15.16000180.3199620
  15.17000200.3337676
  15.18000130.3514860
  15.19000150.3480204
  15.2170.3494628
  .
  .
  20.0000.3118807
  20.0120.3075790
  20.0250.3048350
  20.0370.3090370
  20.0490.3213491
  20.05000110.3106411
  20.06000140.2958525
  20.07000160.2954315
  20.08000180.2988622
  20.0920.2828163
  20.1040.3012785
  20.1160.2912732
  20.1280.3035305
  20.13000110.3047263
  20.14000130.2943486
  20.15000150.2992145
  20.16000180.3017998
  20.1710.3055096
  20.1830.3006694
  20.1950.2961275
  20.2080.2953818
  .
  .




--


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] Pull simulation odditites when viewed in VMD

[Natalie Stephenson]

Thanks loads for that!! I hadn't realised it was that simple!
Natalie
xxx


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: 09 December 2010 12:05
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Pull simulation odditites when viewed in VMD

Natalie Stephenson wrote:
> Hey,
>
> I've been performing a pull simulation of a protein, all seems to work
> fine however after I convert the .xtc file into seperate .gro files and
> load those into VMD to visualise the simulation something weird
> happens.  Every 50 frames or so a random bond within the backbone of the
> protein (not necessarily near the point of pulling or unfolding) seems
> to extend and spike out massively from the structure - does anyone know
> why that would be happening?
>

Please see FAQ #9:

http://www.gromacs.org/Documentation/FAQs

-Justin

> Thanks for your help
> Natalie
>
>

--


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] g_wham

[Nilesh Dhumal]

Hello
I am trying run g_wham for umbrella sampling.

Before going for sampling I want to plot PMF.

I have one .tpr file and one one pullf.xvg. How can I use them to run P

Nilesh

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Re: [gmx-users] g_wham

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello
I am trying run g_wham for umbrella sampling.

Before going for sampling I want to plot PMF.

I have one .tpr file and one one pullf.xvg. How can I use them to run P



You can't.  Umbrella sampling implies that you've done simulations in multiple 
sampling windows along a reaction coordinate.  That's why the input files for 
g_wham are .dat files that list file names of all the .tpr and pullf/x.xvg files 
obtained from these simulations.  There's a tutorial linked from the Gromacs site.


-Justin

--


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] -sel option for g_hbond

[Olga Ivchenko]

Dear Gromacs users,

Does some one know if -sel option for g_hbond command  is working in gromacs
beta 4.5. Because when I try to run fir individual Hbonds privided in second
index file gromacs can not recognize -sel command.

Yours sincerely,
Olga
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[gmx-users] How to force gromacs to fix all bad bonds and angles in a homology model?

[Arthur Roberts]

Hi, all,

I am looking for a way in gromacs or manually to make all the angles,  
etc. ideal.  Perhaps, there is a way to energy minimize a specific  
subset of residues or a single residue.  Your advice would be greatly  
appreciated.


Sincerely,
Art

Dr. Arthur Roberts, Ph.D.
University of California, San Diego
Skaggs School of Pharmacy and Pharmaceutical Sciences
9500 Gilman Drive #0703
La Jolla, CA 92093-0703
email: a1robe...@ucsd.edu
cell: 206-850-7468
office: 858-822-7804
fax: 858-246-0089






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[gmx-users] Re: gmx-users Digest, Vol 80, Issue 64

[shiva birgani]

Dear Justin
So thanks for your help.
you are right. I had put a wrong  .rtp file
With regards
Shiva
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Re: [gmx-users] -sel option for g_hbond

[Justin A. Lemkul]

Olga Ivchenko wrote:

Dear Gromacs users,

Does some one know if -sel option for g_hbond command  is working in 
gromacs beta 4.5. Because when I try to run fir individual Hbonds 
privided in second index file gromacs can not recognize -sel command.




I don't think the -sel option has worked for several years (if it ever did). 
The message in 4.5.3 makes this pretty clear:


"KNOWN PROBLEMS
--
* The option -sel that used to work on selected hbonds is out of order, and
  therefore not available for the time being."

You probably shouldn't be using a beta version; there have been dozens of bug 
fixes that are implemented in the actual release versions.


-Justin


Yours sincerely,
Olga



--


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] How to force gromacs to fix all bad bonds and angles in a homology model?

[Justin A. Lemkul]

Arthur Roberts wrote:

Hi, all,

I am looking for a way in gromacs or manually to make all the angles, 
etc. ideal.  Perhaps, there is a way to energy minimize a specific 
subset of residues or a single residue.  Your advice would be greatly 
appreciated.




Couldn't you just specify very strong force constants for all the bonds, angles, 
etc?  Even in the absence of increased force constants, an in vacuo minimization 
should produce pretty good geometry, should it not?  Using constraints should 
help as well, even perhaps "constraints = all-angles."


To minimize only a subset, you could perhaps freeze the other atoms, but that 
can be tricky depending on the rest of the .mdp settings.  Perhaps a strong 
position restraint on anything you don't want to move?  You can use genrestr 
with a custom index group to specify the atoms to be restrained.


-Justin


Sincerely,
Art

Dr. Arthur Roberts, Ph.D.
University of California, San Diego
Skaggs School of Pharmacy and Pharmaceutical Sciences
9500 Gilman Drive #0703
La Jolla, CA 92093-0703
email: a1robe...@ucsd.edu 
cell: 206-850-7468
office: 858-822-7804
fax: 858-246-0089








--


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] How to obtain the semi-axis lengths from inertia tensor for an aggregate

[sa]

Dear all,

I would to obtain the semi-axis lengths of a simulated micelle (in Ang) with
gromacs. So I have used the g_principal tool (correct ?).  My input command
was

g_principal_mpi -f  bDM-Self_Only_DDM_Center.xtc -s bDM_only.tpr -a1
bDM_Self_Axe1 -a2 bDM_Self_Axe2 -a3 bDM_Self_Axe3 -om bDM_Self_MOI.xvg -dt
10 -b 5 -e 10 < bDM_Mol.txt

Four files *Self_Axe*.dat and bDM_Self_MOI.dat were generated as
expected with four columns. How to deduce the semiaxis lenghts from these
files *Self_Axe*.dat files. The documentation of this tool is not very
clear.

A similar question was posted in the mailing list few days ago,
unfortunately no response was given:

http://www.mail-archive.com/gmx-users@gromacs.org/msg35963.html

Thanks in advance

SA
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[gmx-users] g_anaeig

[pawan raghav]

I am postin ths question second time so please solve this issue
g_anaeig generated numbers of c-alpha or protein structures through -extr
extreme.pdb. The bash shell show numbers of eigenvector structures starting
from first to last frames are as follows

eigenvector   Minimum   Maximum

value   time  value   time

 1   4.88046714148.0   7.74721812501.0

 2   1.63742113926.0   4.34406313110.0

 3  -0.07439312567.0   2.74582614166.0

 4   0.94024012618.0   5.18128314265.0

 5  -2.76056614760.0  -0.10756412789.0

 6   0.39418412627.0   2.69352014997.0

First column shows vectors, but what are the values in second column? Are
they represents energy values in kJ/mol in second and fourth column?

-- 
Pawan
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Re: [gmx-users] g_anaeig

[Justin A. Lemkul]

pawan raghav wrote:

I am postin ths question second time so please solve this issue
g_anaeig generated numbers of c-alpha or protein structures through -extr
extreme.pdb. The bash shell show numbers of eigenvector structures starting
from first to last frames are as follows

eigenvector   Minimum   Maximum

value   time  value   time

 1   4.88046714148.0   7.74721812501.0

 2   1.63742113926.0   4.34406313110.0

 3  -0.07439312567.0   2.74582614166.0

 4   0.94024012618.0   5.18128314265.0

 5  -2.76056614760.0  -0.10756412789.0

 6   0.39418412627.0   2.69352014997.0

First column shows vectors, but what are the values in second column? Are
they represents energy values in kJ/mol in second and fourth column?



A bit of advice: repeated posting of the same question with no additional 
information or evidence that you've tried to learn anything new is generally 
regarded as spam and gets ignored.


Generally, it is a good idea to know what your analysis is doing prior to 
running commands.  It will save you a great deal of stress later trying to sift 
through a mountain of mysterious information.


I had assumed someone would have posted this already, but seeing as they 
haven't, I sifted through my bookmarks and dug up this URL:


http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html

You should find the end of the PCA section particularly applicable.

-Justin


--
Pawan



--


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] CMAP error

[Jon Mujika]

Dear all,

I am setting up a system with GROMACS 4.5.3 and the CHARMM force
field. In the protein, I have a neutral lysine, for which CHARMM force
filed has a specific residue type (LSN). When I wrote LSN as residue
name in the initial pdb file, the topology file was perfectly created
by pdb2gmx. However, in the next step, grompp complained about the
CMAP torsion between the two previous residues:

Fatal error:
Unknown cmap torsion between atoms 2747 2749 2751 2754 2757

However, if the LYS residue was written in the initial pdb file and
the -lys option included with pdb2gmx (chosen the neutral protonation
state for this lysine), grompp did not complain.

The problem is that there is a deprotonated tyrosine (bound to a
metal) in my system. I created a new residue type, but again the
grompp complained about the CMAP between the two previous residues.
Unfortunately, in this case I can't fit the problem with any of the
pdb2gms options.
I think the problem arises when a non-standard residue is included in
the initial pdb file. Does someone else find this problem? I would
appreciate any advise about how to solve it.

Thanks in advance

Jon
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Re: [gmx-users] CMAP error

[Justin A. Lemkul]

Jon Mujika wrote:

Dear all,

I am setting up a system with GROMACS 4.5.3 and the CHARMM force
field. In the protein, I have a neutral lysine, for which CHARMM force
filed has a specific residue type (LSN). When I wrote LSN as residue
name in the initial pdb file, the topology file was perfectly created
by pdb2gmx. However, in the next step, grompp complained about the
CMAP torsion between the two previous residues:

Fatal error:
Unknown cmap torsion between atoms 2747 2749 2751 2754 2757

However, if the LYS residue was written in the initial pdb file and
the -lys option included with pdb2gmx (chosen the neutral protonation
state for this lysine), grompp did not complain.

The problem is that there is a deprotonated tyrosine (bound to a
metal) in my system. I created a new residue type, but again the
grompp complained about the CMAP between the two previous residues.
Unfortunately, in this case I can't fit the problem with any of the
pdb2gms options.
I think the problem arises when a non-standard residue is included in
the initial pdb file. Does someone else find this problem? I would
appreciate any advise about how to solve it.



I can't promise a solution, but you could try adding LSN and whatever other 
non-standard residues you need to use in residuetypes.dat.  I noticed that LSN 
is not there, which seems like an omission, since the other CHARMM-specific 
residue names are there.  When LYS is present, probably pdb2gmx is correctly 
interpreting the residue as protein before converting its name.  In the case of 
LSN or any other non-standard residue, this may not be the case.  Check the 
output of pdb2gmx carefully for any messages that might indicate that a residue 
of type "Other" was detected.  I've had this cause other problems.


If adding LSN to residuetypes.dat fixes the problem, I will file a bugzilla.

-Justin


Thanks in advance

Jon


--


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] CMAP error

[Amit Choubey]

This may not be related but it was not straight forward to do DPPC membrane
simulation using CHARMM FF in gromacs. The DPPC molecule was not defined at
all in the FF files.

The DPPC is defined in terms of two more residues in CHARMM.

amit

On Thu, Dec 9, 2010 at 11:21 AM, Justin A. Lemkul  wrote:

>
>
> Jon Mujika wrote:
>
>> Dear all,
>>
>> I am setting up a system with GROMACS 4.5.3 and the CHARMM force
>> field. In the protein, I have a neutral lysine, for which CHARMM force
>> filed has a specific residue type (LSN). When I wrote LSN as residue
>> name in the initial pdb file, the topology file was perfectly created
>> by pdb2gmx. However, in the next step, grompp complained about the
>> CMAP torsion between the two previous residues:
>>
>> Fatal error:
>> Unknown cmap torsion between atoms 2747 2749 2751 2754 2757
>>
>> However, if the LYS residue was written in the initial pdb file and
>> the -lys option included with pdb2gmx (chosen the neutral protonation
>> state for this lysine), grompp did not complain.
>>
>> The problem is that there is a deprotonated tyrosine (bound to a
>> metal) in my system. I created a new residue type, but again the
>> grompp complained about the CMAP between the two previous residues.
>> Unfortunately, in this case I can't fit the problem with any of the
>> pdb2gms options.
>> I think the problem arises when a non-standard residue is included in
>> the initial pdb file. Does someone else find this problem? I would
>> appreciate any advise about how to solve it.
>>
>>
> I can't promise a solution, but you could try adding LSN and whatever other
> non-standard residues you need to use in residuetypes.dat.  I noticed that
> LSN is not there, which seems like an omission, since the other
> CHARMM-specific residue names are there.  When LYS is present, probably
> pdb2gmx is correctly interpreting the residue as protein before converting
> its name.  In the case of LSN or any other non-standard residue, this may
> not be the case.  Check the output of pdb2gmx carefully for any messages
> that might indicate that a residue of type "Other" was detected.  I've had
> this cause other problems.
>
> If adding LSN to residuetypes.dat fixes the problem, I will file a
> bugzilla.
>
> -Justin
>
>  Thanks in advance
>>
>> Jon
>>
>
> --
> 
>
> 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] CMAP error

[Thomas Piggot]

This is a completely separate issue where the CHARMM force field files 
from which the GROMACS CHARMM27 rtp entries were created do not have a 
DPPC entry, rather DPPC in CHARMM is created from using two residues 
(PALM and PCGL) and two patches (EST1 and EST2). It should have been 
easy enough to make a CHARMM27 DPPC rtp entry anyway.


Cheers

Tom

Amit Choubey wrote:
This may not be related but it was not straight forward to do DPPC 
membrane simulation using CHARMM FF in gromacs. The DPPC molecule was 
not defined at all in the FF files.


The DPPC is defined in terms of two more residues in CHARMM.

amit

On Thu, Dec 9, 2010 at 11:21 AM, Justin A. Lemkul > wrote:




Jon Mujika wrote:

Dear all,

I am setting up a system with GROMACS 4.5.3 and the CHARMM force
field. In the protein, I have a neutral lysine, for which CHARMM
force
filed has a specific residue type (LSN). When I wrote LSN as residue
name in the initial pdb file, the topology file was perfectly
created
by pdb2gmx. However, in the next step, grompp complained about the
CMAP torsion between the two previous residues:

Fatal error:
Unknown cmap torsion between atoms 2747 2749 2751 2754 2757

However, if the LYS residue was written in the initial pdb file and
the -lys option included with pdb2gmx (chosen the neutral
protonation
state for this lysine), grompp did not complain.

The problem is that there is a deprotonated tyrosine (bound to a
metal) in my system. I created a new residue type, but again the
grompp complained about the CMAP between the two previous residues.
Unfortunately, in this case I can't fit the problem with any of the
pdb2gms options.
I think the problem arises when a non-standard residue is
included in
the initial pdb file. Does someone else find this problem? I would
appreciate any advise about how to solve it.


I can't promise a solution, but you could try adding LSN and
whatever other non-standard residues you need to use in
residuetypes.dat.  I noticed that LSN is not there, which seems like
an omission, since the other CHARMM-specific residue names are
there.  When LYS is present, probably pdb2gmx is correctly
interpreting the residue as protein before converting its name.  In
the case of LSN or any other non-standard residue, this may not be
the case.  Check the output of pdb2gmx carefully for any messages
that might indicate that a residue of type "Other" was detected.
 I've had this cause other problems.

If adding LSN to residuetypes.dat fixes the problem, I will file a
bugzilla.

-Justin

Thanks in advance

Jon


-- 



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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University of Southampton, UK.
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[gmx-users] gb_saltconc in implicit water simulations

[Bob Johnson]

Hello everyone,
I am trying to use implicit solvent with a CG DNA model. The model, however,
uses explicit charges, which means that the DNA carries an overall negative
charge. When using implicit solvent with a charged system in other codes
(e.g. Amber), the electrolyte is taken care of implicitly as well. However,
in Gromacs this is currently not implemented since gb_saltconc is always set
to 0. Without any salt, the DNA duplex is obviously unstable. Are there
plans on implementing implicit counterions so that one can set gb_saltconc
to nonzero values?

It doesn't seem natural to include explicit counterions to neutralize the
system when using implicit solvent. Is there a typical protocol one follows
to neutralize charged systems when using implicit solvent?
Thanks,
Bob

-- 
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Institute for Computational Molecular Science
Temple University
1900 North 12th Street
Philadelphia, PA 19122
http://astro.temple.edu/~rjohnson
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[gmx-users] What might be the process if we wanted to sim a peptide + a peptide?

[swati shah]

Dear Gromacs Users,
Can we perform gromacs analysis on any two molecules like peptide+ peptide or 
DNA+ RNA? and what might be the setup and process if we wanted to sim a peptide 
+ a peptide with a small molecule causing a PTM event. If we can do so then do 
we have any options to select two peptides with one or more having PTM 
via small molecule. What might be the sequence of events in this use case.Any 
suggestion??
Thanks,SWati

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Re: [gmx-users] What might be the process if we wanted to sim a peptide + a peptide?

[Justin A. Lemkul]

swati shah wrote:

Dear Gromacs Users,

Can we perform gromacs analysis on any two molecules like peptide+ 
peptide or DNA+ RNA? and what might be the setup and process if we 
wanted to sim a peptide + a peptide with a small molecule causing a PTM 
event. If we can do so then do we have any options to select two 
peptides with one or more having PTM via small molecule. What might be 
the sequence of events in this use case.

Any suggestion??



Your series of questions is extremely broad, especially the use of the phrase 
"Gromacs analysis."  What do you mean?  Do you wish to study the effect of a 
post-translational modification (PTM) on peptide aggregation?  Or binding 
studies of peptides and nucleic acid?


In theory, you can set up just about anything you want.  Gromacs is versatile 
like that.  If you're looking at covalent PTM events, then no, you can't do it 
with classical mechanics, which does not allow for bond breaking or forming.  If 
you want to study the effects of small molecules on aggregation, that's also 
possible.  The conditions depend entirely upon what's known about such a system.


If you ask a more focused, specific question, you're more likely to get a real 
answer.


-Justin


Thanks,
SWati




--


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] Seeking advice on how to build Gromacs on Teragrid resources

[J. Nathan Scott]

Hello gmx users! I realize this may be a touch off topic, but I am
hoping that someone out there can offer some advice on how to build
Gromacs for parallel use on a Teragrid site. Our group is currently
using Abe on Teragrid, and unfortunately the latest version of Gromacs
compiled for public use on Abe is 4.0.2. Apparently installation of
4.5.3 is at least on the to-do list for Abe, but we would very much
like to use 4.5.3 now if we can get this issue figured it out.

I have built a parallel version of mdrun using Abe installed versions
of fftw3 and mvapich2 using the following commands:

setenv CPPFLAGS "-I/usr/apps/math/fftw/fftw-3.1.2/gcc/include/
-I/usr/apps/mpi/marmot_mvapich2_intel/include"
setenv LDFLAGS "-L/usr/apps/math/fftw/fftw-3.1.2/gcc/lib
-L/usr/apps/mpi/marmot_mvapich2_intel/lib"
./configure --enable-mpi --enable-float --prefix=/u/ac/jnscott/gromacs
--program-suffix=_mpi
make -j 8 mdrun && make install-mdrun

My PBS script file looks like the following:

---
#!/bin/csh
#PBS -l nodes=2:ppn=8
#PBS -V
#PBS -o pbs_nvt.out
#PBS -e pbs_nvt.err
#PBS -l walltime=2:00:00
#PBS -N gmx
cd /u/ac/jnscott/1stn/1stn_wt/oplsaa_spce
mvapich2-start-mpd
setenv NP `wc -l ${PBS_NODEFILE} | cut -d'/' -f1`
setenv MV2_SRQ_SIZE 4000
mpirun -np ${NP} mdrun_mpi -s nvt.tpr -o nvt.trr -x nvt.xtc -cpo
nvt.cpt -c nvt.gro -e nvt.edr -g nvt.log -dlb yes
---

Unfortunately my runs always fail in the same manner. The log file
simply ends, as you can see below. It appears that Gromacs is picking
up the correct number of nodes specified in the PBS script, but then
something causes it to quit abruptly with no error message.

---

Initializing Domain Decomposition on 16 nodes
Dynamic load balancing: yes
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.526 nm, LJ-14, atoms 1735 1744
  multi-body bonded interactions: 0.526 nm, Ryckaert-Bell., atoms 1735 1744
Minimum cell size due to bonded interactions: 0.578 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.820 nm
Estimated maximum distance required for P-LINCS: 0.820 nm
This distance will limit the DD cell size, you can override this with -rcon
Guess for relative PME load: 0.27
Will use 10 particle-particle and 6 PME only nodes
This is a guess, check the performance at the end of the log file
Using 6 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 10 cells with a minimum initial size of 1.025 nm
The maximum allowed number of cells is: X 5 Y 5 Z 4
Domain decomposition grid 2 x 5 x 1, separate PME nodes 6
PME domain decomposition: 2 x 3 x 1
Interleaving PP and PME nodes
This is a particle-particle only node

Domain decomposition nodeid 0, coordinates 0 0 0

Using two step summing over 2 groups of on average 5.0 processes

Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.



Will do ordinary reciprocal space Ewald sum.
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's:   NS: 1   Coulomb: 1   LJ: 1
Long Range LJ corr.:  3.3589e-04
System total charge: 0.000
Generated table with 1000 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1000 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1000 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 LJ12.
Tabscale = 500 points/nm

Enabling SPC-like water optimization for 6952 molecules.

Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing x86_64 SSE2 support... present.

Removing pbc first time

Initializing Parallel LINear Constraint Solver


Linking all bonded interactions to atoms
There are 9778 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME

The maximum number of communication pulses is: X 1 Y 2
The minimum size for domain decomposition cells is 0.827 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.35 Y 0.73
The maximum allowed distance for charge groups involved in interactions is:
 non-bonded interactions   1.000 nm
two-body bonded interactions  (-rdd)   1.000 nm
  multi-body bonded interactions  (-rdd)   0.827 nm
  atoms separated by up to 5 constraints  (-rcon)  0.827 nm


Making 2D domain decomposition grid 2 x 5 x 1, home cell index 0 0 0

Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
G. Bussi, D. Donadio and M. Parrinello
Canonical 

Re: [gmx-users] Seeking advice on how to build Gromacs on Teragrid resources

[Mark Abraham]

On 10/12/2010 9:14 AM, J. Nathan Scott wrote:

Hello gmx users! I realize this may be a touch off topic, but I am
hoping that someone out there can offer some advice on how to build
Gromacs for parallel use on a Teragrid site. Our group is currently
using Abe on Teragrid, and unfortunately the latest version of Gromacs
compiled for public use on Abe is 4.0.2. Apparently installation of
4.5.3 is at least on the to-do list for Abe, but we would very much
like to use 4.5.3 now if we can get this issue figured it out.

I have built a parallel version of mdrun using Abe installed versions
of fftw3 and mvapich2 using the following commands:


Certainly MPICH use is discouraged, as GROMACS seems to find some bugs 
in it. I'm not sure about MVAPICH. Certainly you should be sure to be 
using the latest version. Compare with OpenMPI if you can.



setenv CPPFLAGS "-I/usr/apps/math/fftw/fftw-3.1.2/gcc/include/
-I/usr/apps/mpi/marmot_mvapich2_intel/include"
setenv LDFLAGS "-L/usr/apps/math/fftw/fftw-3.1.2/gcc/lib
-L/usr/apps/mpi/marmot_mvapich2_intel/lib"
./configure --enable-mpi --enable-float --prefix=/u/ac/jnscott/gromacs
--program-suffix=_mpi
make -j 8 mdrun&&  make install-mdrun

My PBS script file looks like the following:

---
#!/bin/csh
#PBS -l nodes=2:ppn=8


Simplify the conditions when trying to diagnose a problem - try to run 
on one 8-processor node, or even 1 processor. Your crash is consistent 
with some MPI problem, because (off the top of my head) it seems to 
happen when GROMACS starts to do communication to pass around the input 
data.


Mark


#PBS -V
#PBS -o pbs_nvt.out
#PBS -e pbs_nvt.err
#PBS -l walltime=2:00:00
#PBS -N gmx
cd /u/ac/jnscott/1stn/1stn_wt/oplsaa_spce
mvapich2-start-mpd
setenv NP `wc -l ${PBS_NODEFILE} | cut -d'/' -f1`
setenv MV2_SRQ_SIZE 4000
mpirun -np ${NP} mdrun_mpi -s nvt.tpr -o nvt.trr -x nvt.xtc -cpo
nvt.cpt -c nvt.gro -e nvt.edr -g nvt.log -dlb yes
---

Unfortunately my runs always fail in the same manner. The log file
simply ends, as you can see below. It appears that Gromacs is picking
up the correct number of nodes specified in the PBS script, but then
something causes it to quit abruptly with no error message.

---

Initializing Domain Decomposition on 16 nodes
Dynamic load balancing: yes
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
 two-body bonded interactions: 0.526 nm, LJ-14, atoms 1735 1744
   multi-body bonded interactions: 0.526 nm, Ryckaert-Bell., atoms 1735 1744
Minimum cell size due to bonded interactions: 0.578 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.820 nm
Estimated maximum distance required for P-LINCS: 0.820 nm
This distance will limit the DD cell size, you can override this with -rcon
Guess for relative PME load: 0.27
Will use 10 particle-particle and 6 PME only nodes
This is a guess, check the performance at the end of the log file
Using 6 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 10 cells with a minimum initial size of 1.025 nm
The maximum allowed number of cells is: X 5 Y 5 Z 4
Domain decomposition grid 2 x 5 x 1, separate PME nodes 6
PME domain decomposition: 2 x 3 x 1
Interleaving PP and PME nodes
This is a particle-particle only node

Domain decomposition nodeid 0, coordinates 0 0 0

Using two step summing over 2 groups of on average 5.0 processes

Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.



Will do ordinary reciprocal space Ewald sum.
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's:   NS: 1   Coulomb: 1   LJ: 1
Long Range LJ corr.:  3.3589e-04
System total charge: 0.000
Generated table with 1000 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1000 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1000 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 LJ12.
Tabscale = 500 points/nm

Enabling SPC-like water optimization for 6952 molecules.

Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing x86_64 SSE2 support... present.

Removing pbc first time

Initializing Parallel LINear Constraint Solver


Linking all bonded interactions to atoms
There are 9778 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME

The maximum number of communication pulses is: X 1 Y 2
The minimum size for domain decomposition cells is 0.827 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.35 Y 0.73
The maximum allowed distance for charge groups involve

Re: [gmx-users] How to force gromacs to fix all bad bonds and angles in a homology model?

[Thomas Evangelidis]

This is a bit off-topic but if you want to improve dihedral angles, bond
angles and distances, rotamers along with steric clashes, IMO PyRosetta is
more efficient than GROMACS. I use ClassicRelax protocol with the 'standard'
score function in conjunction with the 'score12' patch ('score12' patch is
not included in the example script) that incorporates terms for ramachandran
and omega angles. The only drawback is that the current version 1.1 does not
allow you to apply distance restraints. This feature will be available in
the new version which will be released sometime in January.

Additional improvements can been done by flipping side-chains to adopt
statistically favourable conformations. SCWRL4 is nice choice and is
recommended for homology models derived from low sequence similarity
templates and BEFORE energy minimization. Great care should also be taken to
preserve side-chain conformation of biologically important residues (i.e. in
the active site of an enzyme). SCWRL4 will probably flip them too, which is
something you wouldn't want. You can correct that by editing the .pdb file
upon processing with SCWRL4. You can also do side chain optimization
manually with the UCSF Chimera GUI.

hope this helps,

Thomas



On 9 December 2010 18:22, Justin A. Lemkul  wrote:

>
>
> Arthur Roberts wrote:
>
>> Hi, all,
>>
>> I am looking for a way in gromacs or manually to make all the angles, etc.
>> ideal.  Perhaps, there is a way to energy minimize a specific subset of
>> residues or a single residue.  Your advice would be greatly appreciated.
>>
>>
> Couldn't you just specify very strong force constants for all the bonds,
> angles, etc?  Even in the absence of increased force constants, an in vacuo
> minimization should produce pretty good geometry, should it not?  Using
> constraints should help as well, even perhaps "constraints = all-angles."
>
> To minimize only a subset, you could perhaps freeze the other atoms, but
> that can be tricky depending on the rest of the .mdp settings.  Perhaps a
> strong position restraint on anything you don't want to move?  You can use
> genrestr with a custom index group to specify the atoms to be restrained.
>
> -Justin
>
>  Sincerely,
>> Art
>>
>> Dr. Arthur Roberts, Ph.D.
>> University of California, San Diego
>> Skaggs School of Pharmacy and Pharmaceutical Sciences
>> 9500 Gilman Drive #0703
>> La Jolla, CA 92093-0703
>> email: a1robe...@ucsd.edu 
>>
>> cell: 206-850-7468
>> office: 858-822-7804
>> fax: 858-246-0089
>>
>>
>>
>>
>>
>>
>>
> --
> 
>
> 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/Support/Mailing_Lists/Search before posting!
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[gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?

[Liu Shiyong]

Hi,

 I just tried G53a6 for protein-RNA simulation. But fatal error shows up.

Opening library file /usr/share/gromacs/top//FF.dat

Select the Force Field:
 0: GROMOS96 43a1 force field
 1: GROMOS96 43a2 force field (improved alkane dihedrals)
 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 6: [DEPRECATED] Gromacs force field (see manual)
 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
 8: Encad all-atom force field, using scaled-down vacuum charges
 9: Encad all-atom force field, using full solvent charges

Best

-- 
Shiyong Liu
--
Biomolecular Physics and Modeling Group, Department of Physics,
Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
Tel：86-27-87558335-805
--
Chinese Version:
--
刘士勇
华中科技大学物理学院  生物物理模建小组
湖北省武汉市洪山区珞瑜路1037号
邮编：430074
电话：86-27-87558335-805
---
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Re: [gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?

[Justin A. Lemkul]

Liu Shiyong wrote:

Hi,

 I just tried G53a6 for protein-RNA simulation. But fatal error shows up.



That's a useless description of the problem.  Exact input and output would be 
necessary to diagnose the problem.  Regardless, the choice of Gromos is a 
particularly bad one for nucleic acid simulations.


http://lists.gromacs.org/pipermail/gmx-users/2010-December/056409.html


Opening library file /usr/share/gromacs/top//FF.dat

Select the Force Field:


You probably don't want any of these force fields.  Ask yourself - what do you 
commonly see in the literature?  Have similar studies been done?  I would 
suggest upgrading to the latest version of Gromacs (4.5.3), which has built-in 
compatibility with CHARMM many AMBER force fields.  Then do some homework and 
decide.


-Justin


 0: GROMOS96 43a1 force field
 1: GROMOS96 43a2 force field (improved alkane dihedrals)
 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 6: [DEPRECATED] Gromacs force field (see manual)
 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
 8: Encad all-atom force field, using scaled-down vacuum charges
 9: Encad all-atom force field, using full solvent charges

Best



--


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: Which FF could be used for protein-RNA MD simulation in GROMACS?

[Vitaly Chaban]

Hey, Shiyong -

I believe your problem is related to X2TOP usage rather than to a
proper force field choice. I'd suggest to start with looking into N2T
files for the below entries.

Cheers.

--
Dr. Vitaly V. Chaban
Rochester, U.S.A.


>  I just tried G53a6 for protein-RNA simulation. But fatal error shows up.
>
> Opening library file /usr/share/gromacs/top//FF.dat
>
> Select the Force Field:
>  0: GROMOS96 43a1 force field
>  1: GROMOS96 43a2 force field (improved alkane dihedrals)
>  2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>  3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>  4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>  5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>  6: [DEPRECATED] Gromacs force field (see manual)
>  7: [DEPRECATED] Gromacs force field with hydrogens for NMR
>  8: Encad all-atom force field, using scaled-down vacuum charges
>  9: Encad all-atom force field, using full solvent charges
>
> Best
>
> --
> Shiyong Liu
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Re: [gmx-users] Re: Which FF could be used for protein-RNA MD simulation in GROMACS?

[Justin A. Lemkul]

Vitaly Chaban wrote:

Hey, Shiyong -

I believe your problem is related to X2TOP usage rather than to a
proper force field choice. I'd suggest to start with looking into N2T
files for the below entries.



The output posted is from pdb2gmx.  It is also unlikely that x2top would be of 
any use for a coordinate file containing protein and RNA, given the complexity 
of such molecules.


-Justin


Cheers.

--
Dr. Vitaly V. Chaban
Rochester, U.S.A.



 I just tried G53a6 for protein-RNA simulation. But fatal error shows up.

Opening library file /usr/share/gromacs/top//FF.dat

Select the Force Field:
 0: GROMOS96 43a1 force field
 1: GROMOS96 43a2 force field (improved alkane dihedrals)
 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 6: [DEPRECATED] Gromacs force field (see manual)
 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
 8: Encad all-atom force field, using scaled-down vacuum charges
 9: Encad all-atom force field, using full solvent charges

Best

--
Shiyong Liu


--


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] Which FF could be used for protein-RNA MD simulation in GROMACS?

[Liu Shiyong]

Thanks. I will upgrade to Version 4.5 and use AMBER.

I like G53a6, but it surprised me without RNA parameter.


On Fri, Dec 10, 2010 at 11:57 AM, Justin A. Lemkul  wrote:
>
>
> Liu Shiyong wrote:
>>
>> Hi,
>>
>>  I just tried G53a6 for protein-RNA simulation. But fatal error shows up.
>>
>
> That's a useless description of the problem.  Exact input and output would
> be necessary to diagnose the problem.  Regardless, the choice of Gromos is a
> particularly bad one for nucleic acid simulations.
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-December/056409.html
>
>> Opening library file /usr/share/gromacs/top//FF.dat
>>
>> Select the Force Field:
>
> You probably don't want any of these force fields.  Ask yourself - what do
> you commonly see in the literature?  Have similar studies been done?  I
> would suggest upgrading to the latest version of Gromacs (4.5.3), which has
> built-in compatibility with CHARMM many AMBER force fields.  Then do some
> homework and decide.
>
> -Justin
>
>>  0: GROMOS96 43a1 force field
>>  1: GROMOS96 43a2 force field (improved alkane dihedrals)
>>  2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>>  3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>>  4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>>  5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>>  6: [DEPRECATED] Gromacs force field (see manual)
>>  7: [DEPRECATED] Gromacs force field with hydrogens for NMR
>>  8: Encad all-atom force field, using scaled-down vacuum charges
>>  9: Encad all-atom force field, using full solvent charges
>>
>> Best
>>
>
> --
> 
>
> 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 list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> or send it to gmx-users-requ...@gromacs.org.
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>



-- 
Shiyong Liu
--
Biomolecular Physics and Modeling Group, Department of Physics,
Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
Tel：86-27-87558335-805
--
Chinese Version:
--
刘士勇
华中科技大学物理学院  生物物理模建小组
湖北省武汉市洪山区珞瑜路1037号
邮编：430074
电话：86-27-87558335-805
---
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[gmx-users] g_anaeig

[pawan raghav]

Dear justin,

Thanks for your useful suggestions but not the right way to post these
things. Anyway Dear I have already read the link mentioned by you and know
very well what does -extr do actually I want to extract some minimum energy
structure for docking studies from 12500 ps to 15000 ps MD trajectory out of
total 15 ns MD run. For this, I have extract structures along 50
eigenvectors structures. Therefore, I want to confirm the values in second
column whether they are energy values or not.

-- 
Pawan
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Re: [gmx-users] Seeking advice on how to build Gromacs on Teragrid resources

[Roland Schulz]

What MVAPICH version are you using?

Are you using a TPR file you know is running fine on some other machine?

Does the 4.5.2 version they installed run correct? If so what is the
configure line they used?

Roland

On Thu, Dec 9, 2010 at 5:14 PM, J. Nathan Scott <
scot...@chemistry.montana.edu> wrote:

> Hello gmx users! I realize this may be a touch off topic, but I am
> hoping that someone out there can offer some advice on how to build
> Gromacs for parallel use on a Teragrid site. Our group is currently
> using Abe on Teragrid, and unfortunately the latest version of Gromacs
> compiled for public use on Abe is 4.0.2. Apparently installation of
> 4.5.3 is at least on the to-do list for Abe, but we would very much
> like to use 4.5.3 now if we can get this issue figured it out.
>
> I have built a parallel version of mdrun using Abe installed versions
> of fftw3 and mvapich2 using the following commands:
>
> setenv CPPFLAGS "-I/usr/apps/math/fftw/fftw-3.1.2/gcc/include/
> -I/usr/apps/mpi/marmot_mvapich2_intel/include"
> setenv LDFLAGS "-L/usr/apps/math/fftw/fftw-3.1.2/gcc/lib
> -L/usr/apps/mpi/marmot_mvapich2_intel/lib"
> ./configure --enable-mpi --enable-float --prefix=/u/ac/jnscott/gromacs
> --program-suffix=_mpi
> make -j 8 mdrun && make install-mdrun
>
> My PBS script file looks like the following:
>
> ---
> #!/bin/csh
> #PBS -l nodes=2:ppn=8
> #PBS -V
> #PBS -o pbs_nvt.out
> #PBS -e pbs_nvt.err
> #PBS -l walltime=2:00:00
> #PBS -N gmx
> cd /u/ac/jnscott/1stn/1stn_wt/oplsaa_spce
> mvapich2-start-mpd
> setenv NP `wc -l ${PBS_NODEFILE} | cut -d'/' -f1`
> setenv MV2_SRQ_SIZE 4000
> mpirun -np ${NP} mdrun_mpi -s nvt.tpr -o nvt.trr -x nvt.xtc -cpo
> nvt.cpt -c nvt.gro -e nvt.edr -g nvt.log -dlb yes
> ---
>
> Unfortunately my runs always fail in the same manner. The log file
> simply ends, as you can see below. It appears that Gromacs is picking
> up the correct number of nodes specified in the PBS script, but then
> something causes it to quit abruptly with no error message.
>
> ---
> 
> Initializing Domain Decomposition on 16 nodes
> Dynamic load balancing: yes
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
>two-body bonded interactions: 0.526 nm, LJ-14, atoms 1735 1744
>  multi-body bonded interactions: 0.526 nm, Ryckaert-Bell., atoms 1735 1744
> Minimum cell size due to bonded interactions: 0.578 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.820 nm
> Estimated maximum distance required for P-LINCS: 0.820 nm
> This distance will limit the DD cell size, you can override this with -rcon
> Guess for relative PME load: 0.27
> Will use 10 particle-particle and 6 PME only nodes
> This is a guess, check the performance at the end of the log file
> Using 6 separate PME nodes
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 10 cells with a minimum initial size of 1.025 nm
> The maximum allowed number of cells is: X 5 Y 5 Z 4
> Domain decomposition grid 2 x 5 x 1, separate PME nodes 6
> PME domain decomposition: 2 x 3 x 1
> Interleaving PP and PME nodes
> This is a particle-particle only node
>
> Domain decomposition nodeid 0, coordinates 0 0 0
>
> Using two step summing over 2 groups of on average 5.0 processes
>
> Table routines are used for coulomb: TRUE
> Table routines are used for vdw: FALSE
> Will do PME sum in reciprocal space.
>
> 
>
> Will do ordinary reciprocal space Ewald sum.
> Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
> Cut-off's:   NS: 1   Coulomb: 1   LJ: 1
> Long Range LJ corr.:  3.3589e-04
> System total charge: 0.000
> Generated table with 1000 data points for Ewald.
> Tabscale = 500 points/nm
> Generated table with 1000 data points for LJ6.
> Tabscale = 500 points/nm
> Generated table with 1000 data points for LJ12.
> Tabscale = 500 points/nm
> Generated table with 1000 data points for 1-4 COUL.
> Tabscale = 500 points/nm
> Generated table with 1000 data points for 1-4 LJ6.
> Tabscale = 500 points/nm
> Generated table with 1000 data points for 1-4 LJ12.
> Tabscale = 500 points/nm
>
> Enabling SPC-like water optimization for 6952 molecules.
>
> Configuring nonbonded kernels...
> Configuring standard C nonbonded kernels...
> Testing x86_64 SSE2 support... present.
>
> Removing pbc first time
>
> Initializing Parallel LINear Constraint Solver
>
> 
> Linking all bonded interactions to atoms
> There are 9778 inter charge-group exclusions,
> will use an extra communication step for exclusion forces for PME
>
> The maximum number of communication pulses is: X 1 Y 2
> The minimum size for domain decomposition cells is 0.827 nm
> The requested allowed shrink of DD cells (option -dds) is: 0.80
> The allowed shrink of domain decomposition cells is: X 0.35 Y 0.73
> The maximum allowed distance for charge groups involved in interactions is:
> non-bo