[gmx-users] Re: A common error Atom O11 in residue bDM 1 was

[ABEL Stephane 175950]

OK you thank Justin for your explanation. Accordingly, I have changed the C* 
and O* atom names in the pdb and now it works. 
 
A bientôt 
 
Stefane


ABEL Stephane 175950 wrote:
> You are right Justin,
>
> The 1O1 atoms and (others 1O2, etc.) are changed to O11, O21, etc. (?). Why
> this problem happens ? Should I change the name of these atoms in the rtp and
> pdb files ? Is a trick is available to avoid this "bad" translation ?
>

The only option is to not use digits as the first characters in an atom name.
The code in pdb2gmx.c calls a function "rename_atoms" in xlate.c, which (since a
value of TRUE is passed to the function for bReorderNum), shifts the position of
all digits in the first position:

 if (bReorderNum)
 {
 if (isdigit(atombuf[0]))
 {
 c = atombuf[0];
 for (i=0; ((size_t)i Stefane
>
>
> ABEL Stephane 175950 wrote:
>> Dear all,
>>
>> I have a very "common" problem when I try to convert a pdb file to a gro
>> file with the following command.
>>
>> I use charmm27ff and gmx4.5.1.
>>
>> pdb2gmx_mpi -f 1-bDM.pdb -o 1-bDM.gro -p 1-bDM.top -chargegrp
>>
>> I obtain the following "commun" error :
>>
>> "Atom O11 in residue bDM 1 was not found in rtp entry bDM with 80 atoms
>> while sorting atoms".
>>
>> I am surprised to have this message, since after verification in the
>> 1-bDM.pdb, I have not found an atom with this name. I have also checked the
>> format of the pdb and all the fields are in right place.
>>
>
> Probably atom 1O1 is being translated as O11.  I have had similar problems
> with translated atom names.  If you add "-debug 1" to your pdb2gmx command
> line, you will get output .pdb files containing the structure as pdb2gmx is
> interpreting it.  That's how I've identified some spurious translations
> before.
>
> -Justin
>
>> Below my PDB file ATOM  1 1C1  bDM 1 -28.807  -8.973  -4.361
>> 0.30  0.00 ATOM  2 H1A  bDM 1 -28.976  -9.551  -3.427  0.10
>> 0.00 ATOM  3 1O1  bDM 1 -27.541  -9.232  -4.796 -0.40  0.00
>> ATOM  4 1C2  bDM 1 -29.836  -9.352  -5.325  0.14  0.00 ATOM
>> 5 H2A  bDM 1 -30.783  -9.324  -4.746  0.09  0.00 ATOM  6 1O2
>> bDM 1 -29.680 -10.694  -5.733 -0.66  0.00 ATOM  7 H2OA bDM
>> 1 -28.731 -10.800  -5.827  0.43  0.00 ATOM  8 1C3  bDM 1
>> -29.990  -8.385  -6.493  0.14  0.00 ATOM  9 H3A  bDM 1 -29.086
>> -8.411  -7.139  0.09  0.00 ATOM 10 1O3  bDM 1 -31.239  -8.585
>> -7.237 -0.66  0.00 ATOM 11 H3OA bDM 1 -31.193  -8.053  -8.035
>> 0.43  0.00 ATOM 12 1C4  bDM 1 -29.957  -6.922  -6.018  0.14
>> 0.00 ATOM 13 H4A  bDM 1 -30.923  -6.772  -5.490  0.09  0.00
>> ATOM 14 1O4  bDM 1 -29.963  -6.003  -7.122 -0.66  0.00 ATOM
>> 15 H4OA bDM 1 -29.993  -5.118  -6.751  0.43  0.00 ATOM 16 1C5
>> bDM 1 -28.865  -6.650  -5.081  0.10  0.00 ATOM 17 H5A  bDM
>> 1 -27.963  -7.009  -5.622  0.10  0.00 ATOM 18 1C6  bDM 1
>> -28.730  -5.254  -4.552  0.05  0.00 ATOM 19 H61A bDM 1 -29.694
>> -5.009  -4.056  0.09  0.00 ATOM 20 H61B bDM 1 -28.509  -4.622
>> -5.438  0.09  0.00 ATOM 21 1O6  bDM 1 -27.593  -5.254  -3.684
>> -0.66  0.00 ATOM 22 H6OA bDM 1 -27.699  -5.900  -2.982  0.43
>> 0.00 ATOM 23 1O5  bDM 1 -28.979  -7.582  -3.963 -0.40  0.00
>> ATOM 24 2C1  bDM 1 -23.620  -9.286  -3.000  0.20  0.00 ATOM
>> 25 H1B  bDM 1 -23.440 -10.274  -3.475  0.09  0.00 ATOM 26 2C2
>> bDM 1 -24.806  -9.283  -2.026  0.14  0.00 ATOM 27 H2B  bDM
>> 1 -24.867  -8.235  -1.662  0.09  0.00 ATOM 28 2O2  bDM 1
>> -24.477 -10.097  -0.884 -0.66  0.00 ATOM 29 H2OB bDM 1 -23.792
>> -9.775  -0.294  0.43  0.00 ATOM 30 2C3  bDM 1 -26.163  -9.642
>> -2.661  0.14  0.00 ATOM 31 H3B  bDM 1 -26.142 -10.663  -3.098
>> 0.09  0.00 ATOM 32 2O3  bDM 1 -27.232  -9.397  -1.722 -0.66
>> 0.00 ATOM 33 H3OB bDM 1 -27.384 -10.156  -1.155  0.43  0.00
>> ATOM 34 2C4  bDM 1 -26.364  -8.872  -3.987  0.10  0.00 ATOM
>> 35 H4B  bDM 1 -26.533  -7.835  -3.626  0.10  0.00 ATOM 36 2C5
>> bDM 1 -25.089  -8.936  -4.892  0.25  0.00 ATOM 37 H5B  bDM
>> 1 -24.906  -9.942  -5.326  0.09  0.00 ATOM 38 2C6  bDM 1
>> -25.225  -7.980  -6.074  0.05  0.00 ATOM 39 H62A bDM 1 -25.159
>> -6.910  -5.780  0.09  0.00 ATOM 40 H62B bDM 1 -26.236  -8.045
>> -6.532  0.09  0.00 ATOM 41 2O5  bDM 1 -24.218  -8.289  -7.105
>> -0.66  0.00 ATOM 42 H5OB bDM 1 -24.661  -8.895  -7.704  0.43
>> 0.00 ATOM 43 2O4  bDM 1 -24.011  -8.432  -4.077 -0.40  0.00
>> ATOM 44 2O1  bDM 1 -22.364  -8.895  -2.386 -0.30  0.00 ATOM
>> 45 C7   bDM 1 -21.159  -9.105  -3.148 -0.11  0.00 ATOM 46 H7A
>> bDM 1 -20.922 -10.188  -3.228  0.09  0.00 

Re: [gmx-users] Query regarding protonation and deprotonation of some residues

[Tsjerk Wassenaar]

Hi Sonali,

First of all, you'll have to find a force field that supports tyrosinate and
serinate. These aren't generally considered titratable and are consequently
not in the list for interactive selections with pdb2gmx. Once you've found a
suitable force field, you'll have to set the protonation states by renaming
the residues. Such simulations are advanced, requiring a thorough knowledge
of simulations and force fields. Do check
http://www.gromacs.org/Documentation/How-tos/Parameterization if you haven't
done so.

Hope it helps,

Tsjerk

On Mon, Sep 27, 2010 at 8:49 AM, sonali dhindwal <
sonali11dhind...@yahoo.co.in> wrote:

> Thanks Kass for the help.
>
> I want to specifically protonate one of the lysine near the active site and
> deprotonate Tyr and Ser. It will be kind if  you can please help me to know
> how to select that specific residue number.
>
> Regards
> --
> Sonali Dhindwal
>
>
> --- On *Mon, 27/9/10, Itamar Kass * wrote:
>
>
> From: Itamar Kass 
> Subject: Re: [gmx-users] Query regarding protonation and deprotonation of
> some residues
> To: "Discussion list for GROMACS users" 
> Date: Monday, 27 September, 2010, 10:07 AM
>
>
> Hi,
>
> You need to define the protonation sate vie pdb2gmx.
>
> pdb2gmx -tyr -lys
>
> On 27/09/10 2:34 PM, sonali dhindwal wrote:
>
>   Hello All,
>
> I came through this research article, in which author has selectively
> deprotonated and protonated some of the residues to simulate the condition
> for electrostatic interaction with the substrate while carrying out
> molecular dynamics simulation.
>
> It will be appreciable, if you could help me regarding the same, how to
> deprotonate Tyr and Ser residue and protonate Lysine residue of the protein
> while preparing the protein topology to be used for molecular dynamics
> simulation in Gromacs.
>
> Thanks and Regards.
>
> --
> Sonali Dhindwal
>
>
> --
>
>
> "In theory, there is no difference between theory and practice. But, in 
> practice, there is." - Jan L.A. van de Snepscheut
>
> ===
> | Itamar Kass, Ph.D.
> | Postdoctoral Research Fellow
> |
> | Department of Biochemistry and Molecular Biology
> | Building 77 Clayton Campus
> | Wellington Road
> | Monash University,
> | Victoria 3800
> | Australia
> |
> | Tel: +61 3 9902 9376
> | Fax: +61 3 9902 9500
> | E-mail: itamar.k...@monash.edu 
> 
>
>
> -Inline Attachment Follows-
>
> --
> 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
>
>
>
> --
> 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!
> 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
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
-- 
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!
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

Re: [gmx-users] Reg: Adding multiple molecules

[Justin A. Lemkul]

vinothkumar mohanakrishnan wrote:

Hi all

I have a diffculty in adding multiple molecules of hexane to my box. my 
box size is 4.72*2.36*2.36 (nm) according to my number density 
calculations the box should fit 124 molecules of hexane whereas it adds 
only 76 molecules to the box below is my command. i had evev tried with 
-try command but without sucess.


genbox -cp hexane-box.gro -ci hexane.gro -p hexane.top -o 
hexane-multi.gro -nmol 124 -seed 1268




If you're not getting all the molecules you want, then genbox is unable to find 
sufficient space for them.  Try a larger box, then equilibrate.


-Justin


Regards
Vinoth



--


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!
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

Re: [gmx-users] How to make a lipid bilayer with specific dimensions?

[Justin A. Lemkul]

NG HUI WEN wrote:

Dear gmxusers,

 

I am trying to make a lipid bilayer with specific dimensions using 
gromacs. So far, I have got up to:


 


1)  Download a lipid POPC128a.pdb from Peter Tieleman’s website

2)  Use genconf –f popc128a.pdb –o popcx2.pdb –nbox 2   2   1 to 
multiply the lipid in the x and y axis. The resultant output was a lipid 
with box vectors 12.478 ,   12.359 and 6.919 (nm)


 

My ultimate aim is to generate a POPC bilayer with the dimensions 
9.600   9.500 and 14.000. Currently, the lipid bilayer is too big. I 


Too big?  If you're using either of the two coordinate files above 
(popc128a.pdb, popcx2.pdb), they should be too small.


would like to “crop” the excess lipids to the required size if at all 
possible. I tried using editconf ( a bit of a long shot) to make a new 
box size. The new structure file has a CRYST1 of 9.600   9.500 and 
14.000 but when I view it with VMD, it is not any smaller than before.


 

Do I have to use other software to achieve this? If so, I’d really 
appreciate some pointers.




You can do this in three steps.  If your goal is to have a single lipid bilayer 
in the middle of the box, with water around it:


genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919
editconf -f popc_new.pdb -o popc_new2.pdb -c -box 9.6 9.5 14
genbox -cp popc_new2.pdb -cs spc216.gro -o solv.pdb

The reason you need three steps is that if you supply a z-dimension of 14 in the 
first genbox command, at least two full bilayers (or some fraction close to it) 
will be placed in your box.  If that's your goal, then this can be done in one step.


-Justin
 


Thanks!

<<

Email has been scanned for viruses by UNMC email management service 



 >>



--


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!
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

[gmx-users] Re: Ask for a question

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.


Most of your questions can be answered by reading molecular modeling textbooks 
or review articles about pulling.  Some of this information is also in the 
manual, so you've certainly missed it.


I would also recommend you read through the COM pulling tutorial I wrote.

http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling

Please post any further questions to the list.

-Justin

zhongjin wrote:

Hello Justin Lemkul,
 I am sorry to trouble you, but I want to ask some questions about COM 
pulling in GMX 4.5.1.
 pull_init1 is the distance between the COMS of reference group and pull group? pull_start = yes means add the COM distance of the starting conformation to pull_init,but 
what is  the COM distance of the starting conformation? pull_rate1 is whose rate?

How to select the eference group? How is the pulling force caculated,and the 
relationship
between pulling force and the coordinats of  reference group and pull group? I 
am sorry to ask your so many questions. I have read the GMX manual, but I am 
very confused.Thanks a lot!

 Best wishes!

Zhongjin He

 



  



--


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!
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

Re: [gmx-users] Reg: Adding multiple molecules

[vinothkumar mohanakrishnan]

Hi justin

if genbox is not able to find sufficient space then why should one calculate
number density for the given box dimension?.similarly the  the number of
molecules are not getting updated in the molecules section of the topology
file when inserting multiple molecules using the genbox command. everytime i
need to update it manually.is there a way to update it automatically?

Regards
Vinoth

On Mon, Sep 27, 2010 at 4:31 PM, Justin A. Lemkul  wrote:

>
>
> vinothkumar mohanakrishnan wrote:
>
>> Hi all
>>
>> I have a diffculty in adding multiple molecules of hexane to my box. my
>> box size is 4.72*2.36*2.36 (nm) according to my number density calculations
>> the box should fit 124 molecules of hexane whereas it adds only 76 molecules
>> to the box below is my command. i had evev tried with -try command but
>> without sucess.
>>
>> genbox -cp hexane-box.gro -ci hexane.gro -p hexane.top -o hexane-multi.gro
>> -nmol 124 -seed 1268
>>
>>
> If you're not getting all the molecules you want, then genbox is unable to
> find sufficient space for them.  Try a larger box, then equilibrate.
>
> -Justin
>
>  Regards
>> Vinoth
>>
>>
> --
> 
>
> 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!
> 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
>
-- 
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!
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

Re: [gmx-users] Reg: Adding multiple molecules

[Justin A. Lemkul]

vinothkumar mohanakrishnan wrote:

Hi justin

if genbox is not able to find sufficient space then why should one 
calculate number density for the given box dimension?.similarly the  the 


Just because you can calculate a certain number density does not necessarily 
mean that the algorithm genbox is using can produce such a configuration.  It 
inserts molecules randomly, so you may be able to find a magical value of -seed 
for which this will work.  The simpler approach is what I suggested earlier.


number of molecules are not getting updated in the molecules section of 
the topology file when inserting multiple molecules using the genbox 
command. everytime i need to update it manually.is  
there a way to update it automatically?




The topology will only be updated automatically when adding water.  Otherwise, 
you have to do it yourself.


-Justin


Regards
Vinoth

On Mon, Sep 27, 2010 at 4:31 PM, Justin A. Lemkul > wrote:




vinothkumar mohanakrishnan wrote:

Hi all

I have a diffculty in adding multiple molecules of hexane to my
box. my box size is 4.72*2.36*2.36 (nm) according to my number
density calculations the box should fit 124 molecules of hexane
whereas it adds only 76 molecules to the box below is my
command. i had evev tried with -try command but without sucess.

genbox -cp hexane-box.gro -ci hexane.gro -p hexane.top -o
hexane-multi.gro -nmol 124 -seed 1268


If you're not getting all the molecules you want, then genbox is
unable to find sufficient space for them.  Try a larger box, then
equilibrate.

-Justin

Regards
Vinoth


-- 



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!
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




--


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!
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

[gmx-users] Pulling Simulation Query

[Natalie Stephenson]

 Hi ...

Just wondering if there's a way, during pulling simulations, to immobilise say 
the C-terminus of the protein.

I've been running through the 'Umbrella Sampling' tutorial with my own protein. 
 Within this tutorial the ChainB is used as the immobile reference - so it is 
this that is position restrained.  Is there a way of position restraining just 
one amino acid? How would I specify that in the topology file?

Thanks
Natalie

-- 
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!
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

Re: [gmx-users] Reg: Adding multiple molecules

[vinothkumar mohanakrishnan]

Hi Justin

Thank you for your suggestion.

Regards
Vinoth

On Mon, Sep 27, 2010 at 4:52 PM, Justin A. Lemkul  wrote:

>
>
> vinothkumar mohanakrishnan wrote:
>
>> Hi justin
>>
>> if genbox is not able to find sufficient space then why should one
>> calculate number density for the given box dimension?.similarly the  the
>>
>
> Just because you can calculate a certain number density does not
> necessarily mean that the algorithm genbox is using can produce such a
> configuration.  It inserts molecules randomly, so you may be able to find a
> magical value of -seed for which this will work.  The simpler approach is
> what I suggested earlier.
>
>  number of molecules are not getting updated in the molecules section of
>> the topology file when inserting multiple molecules using the genbox
>> command. everytime i need to update it manually.is 
>> there a way to update it automatically?
>>
>>
> The topology will only be updated automatically when adding water.
>  Otherwise, you have to do it yourself.
>
> -Justin
>
>  Regards
>> Vinoth
>>
>>
>> On Mon, Sep 27, 2010 at 4:31 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>vinothkumar mohanakrishnan wrote:
>>
>>Hi all
>>
>>I have a diffculty in adding multiple molecules of hexane to my
>>box. my box size is 4.72*2.36*2.36 (nm) according to my number
>>density calculations the box should fit 124 molecules of hexane
>>whereas it adds only 76 molecules to the box below is my
>>command. i had evev tried with -try command but without sucess.
>>
>>genbox -cp hexane-box.gro -ci hexane.gro -p hexane.top -o
>>hexane-multi.gro -nmol 124 -seed 1268
>>
>>
>>If you're not getting all the molecules you want, then genbox is
>>unable to find sufficient space for them.  Try a larger box, then
>>equilibrate.
>>
>>-Justin
>>
>>Regards
>>Vinoth
>>
>>
>>-- 
>>
>>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!
>>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
>>
>>
>>
> --
> 
>
> 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!
> 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
>
-- 
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!
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

Re: [gmx-users] Pulling Simulation Query

[Justin A. Lemkul]

Natalie Stephenson wrote:

 Hi ...

Just wondering if there's a way, during pulling simulations, to 
immobilise say the C-terminus of the protein. 

I've been running through the 'Umbrella Sampling' tutorial with my own 
protein.  Within this tutorial the ChainB is used as the immobile 
reference - so it is this that is position restrained.  Is there a way 
of position restraining just one amino acid? How would I specify that in 
the topology file?




Use genrestr with a custom index group to generate a posre.itp file for that 
residue.  Then, #include this new .itp file in your .top (just like what the 
tutorial does).


-Justin


Thanks
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


--
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!
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

[gmx-users] How to make a lipid bilayer with specific dimensions?

[chris . neale]

I don't think that this is currently causing anybody any problems, but  
note that genbox is going to cut any lipids that cross out of the  
central unit box (either because genbox is unaware of PBC or because  
these lipids now clash across PBC).


Therefore:

genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919

will give you a bilayer that gets solvated with a water defect around  
the edges of the initial unit cell and that, after 10 - 200 ns of  
simulation, gives you an equilibrated bilayer (without water defect)  
that is much smaller than x=9.6, y=9.5.


To get what you want, you need to either start your bilayer with  
larger x and y (calculate area per lipid in 9.6*9.5 to figure out how  
many lipids you should have and keep running genbox until you get  
that), or perhaps a run through inflategro might do it.


Chris.
 --original message --

[gmx-users] How to make a lipid bilayer with specific dimensions?
Justin A. Lemkul jalemkul at vt.edu
Mon Sep 27 13:00:32 CEST 2010

* Previous message: [gmx-users] How to make a lipid bilayer with  
specific dimensions?
* Next message: [gmx-users] Query regarding protonation and  
deprotonation of some residues

* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

NG HUI WEN wrote:

Dear gmxusers,

 I am trying to make a lipid bilayer with specific dimensions using  
gromacs. So far, I have got up to:


 1)  Download a lipid POPC128a.pdb from Peter Tieleman?s website

2)  Use genconf ?f popc128a.pdb ?o popcx2.pdb ?nbox 2   2   1 to  
multiply the lipid in the x and y axis. The resultant output was a  
lipid with box vectors 12.478 ,   12.359 and 6.919 (nm)


 My ultimate aim is to generate a POPC bilayer with the dimensions  
9.600   9.500 and 14.000. Currently, the lipid bilayer is too big. I


Too big?  If you're using either of the two coordinate files above
(popc128a.pdb, popcx2.pdb), they should be too small.

would like to ?crop? the excess lipids to the required size if at  
all possible. I tried using editconf ( a bit of a long shot) to make  
a new box size. The new structure file has a CRYST1 of 9.600   9.500  
and 14.000 but when I view it with VMD, it is not any smaller than  
before.


 Do I have to use other software to achieve this? If so, I?d really  
appreciate some pointers.




You can do this in three steps.  If your goal is to have a single  
lipid bilayer

in the middle of the box, with water around it:

genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919
editconf -f popc_new.pdb -o popc_new2.pdb -c -box 9.6 9.5 14
genbox -cp popc_new2.pdb -cs spc216.gro -o solv.pdb

The reason you need three steps is that if you supply a z-dimension of  
14 in the
first genbox command, at least two full bilayers (or some fraction  
close to it)
will be placed in your box.  If that's your goal, then this can be  
done in one step.


-Justin

 Thanks!

<<

Email has been scanned for viruses by UNMC email management service  



 >>



--


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



* Previous message: [gmx-users] How to make a lipid bilayer with  
specific dimensions?
* Next message: [gmx-users] Query regarding protonation and  
deprotonation of some residues

* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

More information about the gmx-users mailing list


--
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!
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

[gmx-users] Salt concentration

[Anthony Cruz Balberdi]

Dear Users:
I am interested in perform a simulation of a protein in different salt
concentrations. How I can calculate how much Na+ and Cl- ions to
include in the simulation to achieve certain concentration? Could
someone point me in the right direction? Is there a software to do
this type of calculations?

Thanks in advance.

Anthony
-- 
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!
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

Re: [gmx-users] Salt concentration

[Gonçalo C . Justino]

Hi Anthony,

You can use the '-conc' tag from genion during file preparation, as per
http://manual.gromacs.org/current/online/genion.html.

Gonçalo


On 27 September 2010 15:32, Anthony Cruz Balberdi wrote:

> Dear Users:
> I am interested in perform a simulation of a protein in different salt
> concentrations. How I can calculate how much Na+ and Cl- ions to
> include in the simulation to achieve certain concentration? Could
> someone point me in the right direction? Is there a software to do
> this type of calculations?
>
> Thanks in advance.
>
> Anthony
> --
> 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!
> 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
>
-- 
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!
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

[gmx-users] LJ potential

[nishap . patel]

Hello,

  Is there a way to turn off the 6-term in LJ 6-12 potential?

-Nisha P.

--
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!
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

Re: [gmx-users] LJ potential

[David van der Spoel]

On 2010-09-27 18.37, nishap.pa...@utoronto.ca wrote:

Hello,

Is there a way to turn off the 6-term in LJ 6-12 potential?

-Nisha P.


Set the parameters to zero?

--
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 
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

[gmx-users] (no subject)

[Miroslawa aleksandrowa]

Dear users of GROMACS, 
I have a problem with force field . 
Can you tell me what other ff except OPLS-AA I can use for Al3+ or other 
trivalent ions ?
Thank you 
Mira


  
-- 
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!
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

Re: [gmx-users] LJ potential

[nishap . patel]

How can I do that using OPLSAA, because in the nb.itp file the values  
are for sigma/epsilon? Can I change C6=0 in the code file?


Quoting David van der Spoel :


On 2010-09-27 18.37, nishap.pa...@utoronto.ca wrote:

Hello,

Is there a way to turn off the 6-term in LJ 6-12 potential?

-Nisha P.


Set the parameters to zero?

--
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
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





--
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!
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

[gmx-users] MPI and dual-core laptop

[simon sham]

Hi,
I wanted to test the GROMACS MPI version in my dual-processors laptop. I have 
installed openmpi 1.4.2 version. However, when I tried to configure GROMACS 
4.5.1 with --enable-mpi option, I got the following configuration problem:

"checking whether the MPI cc command works... configure: error: Cannot compile 
and link MPI code with mpicc"


mpicc is in my /usr/local/bin directory.

Questions:
1. Can I run GROMACS 4.5.1 in a dual-processor laptop?
2. If yes, how should I configure the software?

Thanks in advance for your insight.

Best,

Simon Sham



  -- 
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!
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

Re: [gmx-users] MPI and dual-core laptop

[Gonçalo C . Justino]

Hi,

My 2 cents on your problem:

I've been running gromacs on nearly everything, from one to six cores. It
works.

Besides mpi being in your /usr/local/bin, is it on the path of your system?

You can do, in the terminal
export PATH=$PATH:/usr/local/bin
Or, for a more permanent solution,
go to your ~/.bashrc file, find a line which already has some PATH folders
in it, and add the :/usr/local/bin and then just retry the configure command
on a new terminal.

Sometimes I need to use different mpi implementations - apparently at
random. Building OpenMPI from source has been the most sucessfully
approach.


Don't know what system you're running, but there any many linux distros
which already include gromacs in the repos.

Hope it helps,
Gonçalo


On 27 September 2010 19:42, simon sham  wrote:

> Hi,
> I wanted to test the GROMACS MPI version in my dual-processors laptop. I
> have installed openmpi 1.4.2 version. However, when I tried to configure
> GROMACS 4.5.1 with --enable-mpi option, I got the following configuration
> problem:
>
> "checking whether the MPI cc command works... configure: error: Cannot
> compile and link MPI code with mpicc"
>
>
> mpicc is in my /usr/local/bin directory.
>
> Questions:
> 1. Can I run GROMACS 4.5.1 in a dual-processor laptop?
> 2. If yes, how should I configure the software?
>
> Thanks in advance for your insight.
>
> Best,
>
> Simon Sham
>
>
> --
> 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!
> 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
>
-- 
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!
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

[gmx-users] g_hbond segmentation fault

[Yao Yao]

--
Found 1048 different hydrogen bonds in trajectory
Found 2292 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
2/10915Segmentation fault
__

Hi guys,

I got the msg like above when I ran g_hbond in version 4.5.
Any guess on the problem?

Thanks,

Yao


  
-- 
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!
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

Re: [gmx-users] Tables with forcefield

[Sai Pooja]

Thanks M!

I am using the standard 6-12 tables available with the gromacs package. For
-table and -tablep options to start with.

I want to understand 1 thing. The forcefield files and the topology file
specifies sigma and epsilon parameters. If I change the combination rule to
1 in the forcefield.itp file, and use tables, how does gromacs convert the
sigma, epsilon values in the topology file to C6 and C12?

Pooja

On Fri, Sep 24, 2010 at 7:07 PM, ms  wrote:

> Hi,
>
> Clarification: I may not be able to help you directly but I can suggest you
> which information you should perhaps give us to enable people more
> knowledgeable than me to help.
>
>
> On 24/09/10 17:33, Sai Pooja wrote:
>
>> I use combination rule 1; but I also define all tabulated interactions for
>>> all possible *pairs* under the [ nonbond_params ] section, so the
>>> combination rule actually doesn't matter much.
>>>
>>
>>
>> Are you suggesting that I can change the combination rule in the
>> forcefield.itp file but I must also supply a table for pairs using -tablep
>> option for this to work?
>>
>
> I am not "suggesting": I am only saying what I am doing :)
>
>
>  Does this mean that one cannot use tables with forcefield parameters?
>>>


>>>
>> Clarification: I want to use forcefield parameters with user defined
>> tables
>> i.e. I want to use sigma and epsilon values generated by pdb2gmx along
>> with a user-defined modified potential energy function using tables.
>>
>
> This is absolutely doable -I do it everyday, in fact. So, don't despair. :)
>
> Now, it seems that you talked about a problem with convergence of the
> SETTLE algorithm. I know little about it, but, couldn't it simply be that
> your tables are "wrong" (that is, they don't play well with algorithms?)
> What is their shape, actually, and on which atomtypes/groups are you
> applying your table? What is the forcefield you are using along with the
> table?
>
> M.
>
> --
> 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!
> 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
>



-- 
Quaerendo Invenietis-Seek and you shall discover.
-- 
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!
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

Re: [gmx-users] g_hbond segmentation fault

[Erik Marklund]

 Yao Yao skrev 2010-09-27 21.22:

--
Found 1048 different hydrogen bonds in trajectory
Found 2292 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
2/10915Segmentation fault
__

Hi guys,

I got the msg like above when I ran g_hbond in version 4.5.
Any guess on the problem?

Thanks,

Yao




What was the command line?

--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@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 
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

[gmx-users] Hardware-specific crash with 4.5.1

[Justin A. Lemkul]

Hi All,

I'm hoping I might get some tips in tracking down the source of an issue that 
appears to be hardware-specific, leading to crashes in my system.  The failures 
are occurring on our supercomputer (Mac OSX 10.3, PowerPC).  Running the same 
.tpr file on my laptop (Mac OSX 10.5.8, Intel Core2Duo) and on another 
workstation (Ubuntu 10.04, AMD64) produce identical results.  I suspect the 
problem stems from unsuccessful energy minimization, which then leads to a crash 
when running full MD.  All jobs were run in parallel on two cores.  The 
supercomputer does not support threading, so MPI is invoked using MPICH-1.2.5 
(native MPI implementation on the cluster).



Details as follows:

EM md.log file: successful run (Intel Core2Duo or AMD64)

Steepest Descents converged to Fmax < 1000 in 7 steps
Potential Energy  = -4.8878180e+04
Maximum force =  8.7791553e+02 on atom 5440
Norm of force =  1.1781271e+02


EM md.log file: unsuccessful run (PowerPC)

Steepest Descents converged to Fmax < 1000 in 1 steps
Potential Energy  = -2.4873273e+04
Maximum force =  0.000e+00 on atom 0
Norm of force =nan


MD invoked from the minimized structure generated on my laptop or AMD64 runs 
successfully (at least for a few hundred steps in my test), but the MD on the 
PowerPC cluster fails immediately:


   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
U-BProper Dih.  Improper Dih.  CMAP Dih.GB Polarization
7.93559e+039.34958e+032.24036e+02   -2.47750e+03   -7.83599e+04
  LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)  Potential
7.70042e+039.94520e+04   -1.17168e+04   -5.79783e+04   -2.55780e+04
Kinetic En.   Total EnergyTemperature Pressure (bar)   Constr. rmsd
nannannan0.0e+00nan
  Constr.2 rmsd
nan

DD  step 9 load imb.: force  3.0%


---
Program mdrun_4.5.1_mpi, VERSION 4.5.1
Source code file: nsgrid.c, line: 601

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ind has value 7131. It should have been within [ 0 .. 7131 ]

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

It seems as if the crash really shouldn't be happening, if the value range is 
inclusive.


Running with all-vs-all kernels works, but the performance is horrendously slow 
(<300 ps per day for a 7131-atom system) so I am attempting to use long cutoffs 
(2.0 nm) as others on the list have suggested.


Details of the installations and .mdp files are appended below.

-Justin

=== em.mdp ===
; Run parameters
integrator  = steep ; EM
emstep  = 0.005
emtol   = 1000
nsteps  = 5
nstcomm = 1
comm_mode   = angular   ; non-periodic system
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= no; starting up
; required cutoffs for implicit
nstlist = 1
ns_type = grid
rlist   = 2.0
rcoulomb= 2.0
rvdw= 2.0
; cutoffs required for qq and vdw
coulombtype = cut-off
vdwtype = cut-off
; temperature coupling
tcoupl  = no
; Pressure coupling is off
Pcoupl  = no
; Periodic boundary conditions are off for implicit
pbc = no
; Settings for implicit solvent
implicit_solvent= GBSA
gb_algorithm= OBC
rgbradii= 2.0


=== md.mdp ===

; Run parameters
integrator  = sd; velocity Langevin dynamics
dt  = 0.002
nsteps  = 250   ; 5000 ps (5 ns)
nstcomm = 1
comm_mode   = angular   ; non-periodic system
; Output parameters
nstxout = 0 ; nst[xvf]out = 0 to suppress useless .trr 
output
nstvout = 0
nstfout = 0
nstlog  = 5000  ; 10 ps
nstenergy   = 5000  ; 10 ps
nstxtcout   = 5000  ; 10 ps
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= no; starting up
; required cutoffs for implicit
nstlist = 10
ns_type = grid
rlist   = 2.0
rcoulomb= 2.0
rvdw= 2.0
; cutoffs required for qq and vdw
coulombtype = cut-off
vdwtype = cut-off
; temperature coupling
tc_grps = System
tau

RE: [gmx-users] Salt concentration

[Dallas Warren]

Calculator or spreadsheet will do the job fine.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Anthony Cruz Balberdi
> Sent: Tuesday, 28 September 2010 12:33 AM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] Salt concentration
> 
> Dear Users:
> I am interested in perform a simulation of a protein in different salt
> concentrations. How I can calculate how much Na+ and Cl- ions to
> include in the simulation to achieve certain concentration? Could
> someone point me in the right direction? Is there a software to do
> this type of calculations?
> 
> Thanks in advance.
> 
> Anthony
> --
> 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!
> 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
--
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!
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

[gmx-users] Gromacs 4.0.7 failing in parallel mode

[Jyoti Mahalik]

Hi,
 I am simulating two protein units in water and it works fine in the  
single processor but when I use the parallel version of the GROMACS,  
it fails.


My script:
grompp_mpi_d -f md.mdp -c hba_b4md.gro -r hba_b4md.gro -p hba.top -o  
hba_md.tpr
mpirun -np $NPROCS mdrun_mpi_d -np $NPROCS -ddorder pp_pme -s  
hba_md.tpr -o hba_md.trr -c hba_pmd.gro -g md.log -e md. edr


Error Messages:
Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max inf (between atoms 1 and 2)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  1  2   90.00.1000  inf  0.1000
712714   90.00.1250  inf  0.1250
712713   90.00.1250  inf  0.1250
710711   90.00.1000  inf  0.1000
709710   90.00.1430  inf  0.1430


Program mdrun_mpi_d, VERSION 4.0.7
Source code file: constr.c, line: 136

Fatal error:
Too many LINCS warnings (1286)
If you know what you are doing you can adjust the lincs warning  
threshold in your mdp file

or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem



Regards,
JP Mahalik
--
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!
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

Re: [gmx-users] Gromacs 4.0.7 failing in parallel mode

[Mark Abraham]

- Original Message -
From: Jyoti Mahalik 
Date: Tuesday, September 28, 2010 9:19
Subject: [gmx-users] Gromacs 4.0.7 failing in parallel mode
To: gmx-users@gromacs.org

> Hi,
>  I am simulating two protein units in water and it works 
> fine in the single processor but when I use the parallel version 
> of the GROMACS, it fails.
> 
> My script:
> grompp_mpi_d -f md.mdp -c hba_b4md.gro -r hba_b4md.gro -p 
> hba.top -o hba_md.tpr
> mpirun -np $NPROCS mdrun_mpi_d -np $NPROCS -ddorder pp_pme -s 
> hba_md.tpr -o hba_md.trr -c hba_pmd.gro -g md.log -e md. edr
> 
> Error Messages:
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms nan, max inf (between atoms 1 and 2)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, 
> constraint length
>   1  
> 2   90.0
> 0.1000  inf  0.1000
> 712714   
> 90.00.1250  
> inf  0.1250
> 712713   
> 90.00.1250  
> inf  0.1250
> 710711   
> 90.00.1000  
> inf  0.1000
> 709710   
> 90.00.1430  
> inf  0.1430
> 
> 
> Program mdrun_mpi_d, VERSION 4.0.7
> Source code file: constr.c, line: 136
> 
> Fatal error:
> Too many LINCS warnings (1286)
> If you know what you are doing you can adjust the lincs warning 
> threshold in your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem

See http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

Probably your single processor version was also fairly unhappy, but was lucky 
enough to succeed. Reconsider your system preparation workflow in the light of 
the "blowing up" page on the above link.

Mark

-- 
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!
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

Re: [gmx-users] Hardware-specific crash with 4.5.1

[Roland Schulz]

Justin,

I think the interaction kernel is not OK on your PowerPC machine. I assume
that from: 1) The force seems to be zero (minimization output). 2) When you
use the all-to-all kernel which is not available for the powerpc kernel, it
automatically falls back to the C kernel and then it works.

What is the kernel you are using? It should say in the log file. Look
for: "Configuring single precision IBM Power6-specific Fortran kernels" or
"Testing Altivec/VMX support"

You can also look in the config.h whether  GMX_POWER6 and/or GMX_PPC_ALTIVEC
is set. I suggest you try to compile with one/both of them deactivated and
see whether that solves it. This will make it slower too. Thus if this is
indeed the problem, you will probably want to figure out why the fastest
kernel doesn't work correctly to get good performance.

Roland


On Mon, Sep 27, 2010 at 4:59 PM, Justin A. Lemkul  wrote:

>
> Hi All,
>
> I'm hoping I might get some tips in tracking down the source of an issue
> that appears to be hardware-specific, leading to crashes in my system.  The
> failures are occurring on our supercomputer (Mac OSX 10.3, PowerPC).
>  Running the same .tpr file on my laptop (Mac OSX 10.5.8, Intel Core2Duo)
> and on another workstation (Ubuntu 10.04, AMD64) produce identical results.
>  I suspect the problem stems from unsuccessful energy minimization, which
> then leads to a crash when running full MD.  All jobs were run in parallel
> on two cores.  The supercomputer does not support threading, so MPI is
> invoked using MPICH-1.2.5 (native MPI implementation on the cluster).
>
>
> Details as follows:
>
> EM md.log file: successful run (Intel Core2Duo or AMD64)
>
> Steepest Descents converged to Fmax < 1000 in 7 steps
> Potential Energy  = -4.8878180e+04
> Maximum force =  8.7791553e+02 on atom 5440
> Norm of force =  1.1781271e+02
>
>
> EM md.log file: unsuccessful run (PowerPC)
>
> Steepest Descents converged to Fmax < 1000 in 1 steps
> Potential Energy  = -2.4873273e+04
> Maximum force =  0.000e+00 on atom 0
> Norm of force =nan
>
>
> MD invoked from the minimized structure generated on my laptop or AMD64
> runs successfully (at least for a few hundred steps in my test), but the MD
> on the PowerPC cluster fails immediately:
>
>   Step   Time Lambda
>  00.00.0
>
>   Energies (kJ/mol)
>U-BProper Dih.  Improper Dih.  CMAP Dih.GB Polarization
>7.93559e+039.34958e+032.24036e+02   -2.47750e+03   -7.83599e+04
>  LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)  Potential
>7.70042e+039.94520e+04   -1.17168e+04   -5.79783e+04   -2.55780e+04
>Kinetic En.   Total EnergyTemperature Pressure (bar)   Constr. rmsd
>nannannan0.0e+00nan
>  Constr.2 rmsd
>nan
>
> DD  step 9 load imb.: force  3.0%
>
>
> ---
> Program mdrun_4.5.1_mpi, VERSION 4.5.1
> Source code file: nsgrid.c, line: 601
>
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
> Variable ind has value 7131. It should have been within [ 0 .. 7131 ]
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> It seems as if the crash really shouldn't be happening, if the value range
> is inclusive.
>
> Running with all-vs-all kernels works, but the performance is horrendously
> slow (<300 ps per day for a 7131-atom system) so I am attempting to use long
> cutoffs (2.0 nm) as others on the list have suggested.
>
> Details of the installations and .mdp files are appended below.
>
> -Justin
>
> === em.mdp ===
> ; Run parameters
> integrator  = steep ; EM
> emstep  = 0.005
> emtol   = 1000
> nsteps  = 5
> nstcomm = 1
> comm_mode   = angular   ; non-periodic system
> ; Bond parameters
> constraint_algorithm= lincs
> constraints = all-bonds
> continuation= no; starting up
> ; required cutoffs for implicit
> nstlist = 1
> ns_type = grid
> rlist   = 2.0
> rcoulomb= 2.0
> rvdw= 2.0
> ; cutoffs required for qq and vdw
> coulombtype = cut-off
> vdwtype = cut-off
> ; temperature coupling
> tcoupl  = no
> ; Pressure coupling is off
> Pcoupl  = no
> ; Periodic boundary conditions are off 

[gmx-users] Psuedo ONIOM gromacs MD run

[TJ Mustard]

  

  
 

Hello all,

 

Is it possible to do a pseudo ONIOM MD run where you hold all atoms rigid except for a small sphere of some radius. I was wondering if I could do this with posres.itp files or a define argument. It would be beneficial if the atoms held rigid had no energies, trajectories, vectors, etc calculated for them as to speed up calculations. I was thinking of first minimizing the energy of the system before restricting the system.

 

 

I came upon this idea first as a "box" inside your solvent md box that held all atoms and bonds that the box's planes intersected with and held those rigid allowing the atoms on the outside of the box to be rigid or removed and the atoms on the inside to be dynamic.

 

Is this possible? I was hoping to test this as a possible promoter of FEP. Of course this could increase or implement artifacts.

 
Thank you, 



 

TJ Mustard
Email: musta...@onid.orst.edu
  

-- 
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!
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

Re: [gmx-users] Psuedo ONIOM gromacs MD run

[Mark Abraham]

Freeze groups do something along these lines. See manual.

Mark

- Original Message -
From: TJ Mustard 
Date: Tuesday, September 28, 2010 10:46
Subject: [gmx-users] Psuedo ONIOM gromacs MD run
To: "gmx-users@gromacs.org" 

  
---
| 

 
>  
  Hello all,
   
  Is it possible to do a pseudo ONIOM MD run where you hold all atoms rigid 
except for a small sphere of some radius. I was wondering if I could do this 
with posres.itp files or a define argument. It would be beneficial if the atoms 
held rigid had no energies, trajectories, vectors, etc calculated for them as 
to speed up calculations. I was thinking of first minimizing the energy of the 
system before restricting the system.
   
   
  I came upon this idea first as a "box" inside your solvent md box that 
held all atoms and bonds that the box's planes intersected with and held those 
rigid allowing the atoms on the outside of the box to be rigid or removed and 
the atoms on the inside to be dynamic.
   
  Is this possible? I was hoping to test this as a possible promoter of 
FEP. Of course this could increase or implement artifacts.
   
 Thank you,   
   
  TJ Mustard
>  Email: musta...@onid.orst.edu
|
---
  > -- 
> 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!
> 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


-- 
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!
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

Re: [gmx-users] Hardware-specific crash with 4.5.1

[Justin A. Lemkul]

Roland Schulz wrote:

Justin,

I think the interaction kernel is not OK on your PowerPC machine. I 
assume that from: 1) The force seems to be zero (minimization output). 
2) When you use the all-to-all kernel which is not available for the 
powerpc kernel, it automatically falls back to the C kernel and then it 
works.




Sounds about right.

What is the kernel you are using? It should say in the log file. Look 
for: "Configuring single precision IBM Power6-specific Fortran kernels" 
or "Testing Altivec/VMX support"




I'm not finding either in the config.log - weird?

You can also look in the config.h whether  GMX_POWER6 
and/or GMX_PPC_ALTIVEC is set. I suggest you try to compile with 
one/both of them deactivated and see whether that solves it. This will 
make it slower too. Thus if this is indeed the problem, you will 
probably want to figure out why the fastest kernel doesn't work 
correctly to get good performance.




It looks like GMX_PPC_ALTIVEC is set.  I suppose I could re-compile with this 
turned off.


Here's what's even weirder.  The problematic version was compiled using the 
standard autoconf procedure.  If I use a CMake-compiled version, the energy 
minimization runs fine, giving the same results (energy and force) as the two 
systems I know are good.  So I guess there's something wrong with the way 
autoconf installed Gromacs.  Perhaps this isn't of concern since Gromacs will 
require CMake in subsequent releases, but I figure I should at least report it 
in case it affects anyone else.


If I may tack one more question on here, I'm wondering why my CMake installation 
 doesn't actually appear to be using MPI.  I get the right result, but the 
problem is, I get a .log, .edr, and .trr for every processor that's being used, 
as if each processor is being given its own job and not distributing the work. 
Here's how I compiled my MPI mdrun, version 4.5.1:


cmake ../gromacs-4.5.1 
-DFFTW3F_LIBRARIES=/home/rdiv1001/fftw-3.0.1-osx/lib/libfftw3f.a 
-DFFTW3F_INCLUDE_DIR=/home/rdiv1001/fftw-3.0.1-osx/include/ 
-DCMAKE_INSTALL_PREFIX=/home/rdiv1001/gromacs-4.5_cmake-osx 
-DGMX_BINARY_SUFFIX=_4.5_cmake_mpi -DGMX_THREADS=OFF -DBUILD_SHARED_LIBS=OFF 
-DGMX_X11=OFF -DGMX_MPI=ON 
-DMPI_COMPILER=/home/rdiv1001/compilers/openmpi-1.2.3-osx/bin/mpicxx 
-DMPI_INCLUDE_PATH=/home/rdiv1001/compilers/openmpi-1.2.3-osx/include


$ make mdrun

$ make install-mdrun

Is there anything obviously wrong with those commands?  Is there any way I 
should know (before actually using mdrun) whether or not I've done things right?


-Justin


Roland


On Mon, Sep 27, 2010 at 4:59 PM, Justin A. Lemkul > wrote:



Hi All,

I'm hoping I might get some tips in tracking down the source of an
issue that appears to be hardware-specific, leading to crashes in my
system.  The failures are occurring on our supercomputer (Mac OSX
10.3, PowerPC).  Running the same .tpr file on my laptop (Mac OSX
10.5.8, Intel Core2Duo) and on another workstation (Ubuntu 10.04,
AMD64) produce identical results.  I suspect the problem stems from
unsuccessful energy minimization, which then leads to a crash when
running full MD.  All jobs were run in parallel on two cores.  The
supercomputer does not support threading, so MPI is invoked using
MPICH-1.2.5 (native MPI implementation on the cluster).


Details as follows:

EM md.log file: successful run (Intel Core2Duo or AMD64)

Steepest Descents converged to Fmax < 1000 in 7 steps
Potential Energy  = -4.8878180e+04
Maximum force =  8.7791553e+02 on atom 5440
Norm of force =  1.1781271e+02


EM md.log file: unsuccessful run (PowerPC)

Steepest Descents converged to Fmax < 1000 in 1 steps
Potential Energy  = -2.4873273e+04
Maximum force =  0.000e+00 on atom 0
Norm of force =nan


MD invoked from the minimized structure generated on my laptop or
AMD64 runs successfully (at least for a few hundred steps in my
test), but the MD on the PowerPC cluster fails immediately:

  Step   Time Lambda
 00.00.0

  Energies (kJ/mol)
   U-BProper Dih.  Improper Dih.  CMAP Dih.GB
Polarization
   7.93559e+039.34958e+032.24036e+02   -2.47750e+03  
-7.83599e+04
 LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)
 Potential
   7.70042e+039.94520e+04   -1.17168e+04   -5.79783e+04  
-2.55780e+04
   Kinetic En.   Total EnergyTemperature Pressure (bar)  
Constr. rmsd
   nannannan0.0e+00
   nan

 Constr.2 rmsd
   nan

DD  step 9 load imb.: force  3.0%


---
Program mdrun_4.5.1_mpi, VERSION 4.5.1
Source code file: nsgrid.c, line: 601

Range checking error:
Explanation: During nei

Re: [gmx-users] Psuedo ONIOM gromacs MD run

[TJ Mustard]

  

  
Thanks Mark I will. I have found that the more I learn about gromacs the less I know about grimacs.


  
   On September 28, 2010 at 2:52 AM Mark Abraham  wrote:
  

  
Freeze groups do something along these lines. See manual.

 Mark

 - Original Message -
 From: TJ Mustard 
 Date: Tuesday, September 28, 2010 10:46
 Subject: [gmx-users] Psuedo ONIOM gromacs MD run
 To: "gmx-users@gromacs.org" 

  

 


  

  
 

>  

Hello all,

 

Is it possible to do a pseudo ONIOM MD run where you hold all atoms rigid except for a small sphere of some radius. I was wondering if I could do this with posres.itp files or a define argument. It would be beneficial if the atoms held rigid had no energies, trajectories, vectors, etc calculated for them as to speed up calculations. I was thinking of first minimizing the energy of the system before restricting the system.

 

 

I came upon this idea first as a "box" inside your solvent md box that held all atoms and bonds that the box's planes intersected with and held those rigid allowing the atoms on the outside of the box to be rigid or removed and the atoms on the inside to be dynamic.

 

Is this possible? I was hoping to test this as a possible promoter of FEP. Of course this could increase or implement artifacts.

 
Thank you, 



 

TJ Mustard
 > Email: musta...@onid.orst.edu
  

  


 > --
 > 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
  


 

TJ Mustard
Email: musta...@onid.orst.edu
  

-- 
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!
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

[gmx-users] Another error that keeps comming up.

[TJ Mustard]

  

  
Hey all,

 

Here is another error that I keep getting. I am trying to "speed up" my md runs with -heavyh and longer time steps. I don't get LINCS errors but I do get this...

 

 

 

Back Off! I just backed up prlog.log to ./#prlog.log.1#
Getting Loaded...
Reading file monomer_pr.tpr, VERSION 4.5.1 (single precision)
Starting 2 threads
Loaded with Money

Making 1D domain decomposition 2 x 1 x 1

Back Off! I just backed up pr.edr to ./#pr.edr.1#
starting mdrun 'Protein in water'
25000 steps,    100.0 ps.
step 900, will finish Mon Sep 27 18:19:07 2010imb F 18%
NOTE: Turning on dynamic load balancing

step 1600, will finish Mon Sep 27 18:18:42 2010vol 0.92  imb F  1%
A list of missing interactions:
    LJC Pairs NB of    278 missing  1
  exclusions of   6966 missing  1

---
Program g4.5.1-mdrun, VERSION 4.5.1
Source code file: domdec_top.c, line: 173

Software inconsistency error:
Some interactions seem to be assigned multiple times
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

 

 

Some settings:

 

define   = -DPOSRES

dt   = 0.004
nsteps   = 25000

 

 

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME  ; = Cutoff
rcoulomb-switch  = 0    ; = 0
rcoulomb = 0.9  ; = 1
; Relative dielectric constant for the medium and the reaction field
epsilon_r    = 1    ; = 1
epsilon_rf   = 1    ; = 1
; Method for doing Van der Waals
vdw-type = Cut-off  ; = Cut-off
; cut-off lengths  
rvdw-switch  = 0    ; = 0
rvdw = 1    ; = 1
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No   ; = No
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1    ; = 1
; Seperate tables between energy group pairs
energygrp_table  =  ; =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12 ; = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0    ; = 0
fourier_ny   = 0    ; = 0
fourier_nz   = 0    ; = 0
; EWALD/PME/PPPM parameters
pme_order    = 6    ; = 4
ewald_rtol   = 1e-05    ; = 1e-05
ewald_geometry   = 3d   ; = 3d
epsilon_surface  = 0    ; = 0
optimize_fft = yes  ; = no

 

 

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling 
tcoupl   = v-rescale    ; = No
nsttcouple   = -1   ; = -1
nh-chain-length  = 10   ; = 10
; Groups to couple separately
tc-grps  = RNA SOL  ; =
; Time constant (ps) and reference temperature (K)
tau-t    = 0.1 0.1  ; =
ref-t    = 300 300  ; =
; Pressure coupling
Pcoupl   = Parrinello-Rahman    ; = No
Pcoupltype   = Isotropic
nstpcouple   = -1   ; = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p    = 1    ; = 1
compressibility  = 4.5e-5   ; =
ref-p    = 1.0  ; =
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = No   ; = No
; Random seed for Andersen thermostat
andersen_seed    = 815131   ; = 815131

 

 

gen-vel  = yes  ; = no
gen-temp = 300  ; = 300
gen-seed = 173529   ; = 173529

 

 

constraints  = all-bonds

 

Any help would be appreciated. It also seems to be intermittent as I have 21 identical runs (with different lambda values) and some work and some don't. It also changes every time I run them.

Thank you,

TJ Mustard
Email: musta...@onid.orst.edu
  

-- 
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!
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

Re: [gmx-users] Hardware-specific crash with 4.5.1

[Mark Abraham]

- Original Message -
From: "Justin A. Lemkul" 
Date: Tuesday, September 28, 2010 11:11
Subject: Re: [gmx-users] Hardware-specific crash with 4.5.1
To: Gromacs Users' List 

> 
> 
> Roland Schulz wrote:
> >Justin,
> >
> >I think the interaction kernel is not OK on your PowerPC 
> machine. I assume that from: 1) The force seems to be zero 
> (minimization output). 2) When you use the all-to-all kernel 
> which is not available for the powerpc kernel, it automatically 
> falls back to the C kernel and then it works.
> >
> 
> Sounds about right.
> 
> >What is the kernel you are using? It should say in the log 
> file. Look for: "Configuring single precision IBM Power6-
> specific Fortran kernels" or "Testing Altivec/VMX support"
> >
> 
> I'm not finding either in the config.log - weird?

You were meant to look in the mdrun.log for runtime confirmation of what 
kernels GROMACS has decided to use.
 
> >You can also look in the config.h whether  GMX_POWER6 
> and/or GMX_PPC_ALTIVEC is set. I suggest you try to compile with 
> one/both of them deactivated and see whether that solves it. 
> This will make it slower too. Thus if this is indeed the 
> problem, you will probably want to figure out why the fastest 
> kernel doesn't work correctly to get good performance.
> >
> 
> It looks like GMX_PPC_ALTIVEC is set.  I suppose I could re-
> compile with this turned off.

This is supposed to be fine for Mac, as I understand.

> Here's what's even weirder.  The problematic version was 
> compiled using the standard autoconf procedure.  If I use a 
> CMake-compiled version, the energy minimization runs fine, 
> giving the same results (energy and force) as the two systems I 
> know are good.  So I guess there's something wrong with the 
> way autoconf installed Gromacs.  Perhaps this isn't of 
> concern since Gromacs will require CMake in subsequent releases, 
> but I figure I should at least report it in case it affects 
> anyone else.
> 
> If I may tack one more question on here, I'm wondering why my 
> CMake installation  doesn't actually appear to be using 
> MPI.  I get the right result, but the problem is, I get a 
> .log, .edr, and .trr for every processor that's being used, as 
> if each processor is being given its own job and not 
> distributing the work. Here's how I compiled my MPI mdrun, 
> version 4.5.1:

At the start and end of the .log files you should get indicators about how many 
MPI processes were actually being used.
 
> cmake ../gromacs-4.5.1 -DFFTW3F_LIBRARIES=/home/rdiv1001/fftw-
> 3.0.1-osx/lib/libfftw3f.a -
> DFFTW3F_INCLUDE_DIR=/home/rdiv1001/fftw-3.0.1-osx/include/ -
> DCMAKE_INSTALL_PREFIX=/home/rdiv1001/gromacs-4.5_cmake-osx -
> DGMX_BINARY_SUFFIX=_4.5_cmake_mpi -DGMX_THREADS=OFF -
> DBUILD_SHARED_LIBS=OFF -DGMX_X11=OFF -DGMX_MPI=ON -
> DMPI_COMPILER=/home/rdiv1001/compilers/openmpi-1.2.3-
> osx/bin/mpicxx -
> DMPI_INCLUDE_PATH=/home/rdiv1001/compilers/openmpi-1.2.3-osx/include
> 
> $ make mdrun
> 
> $ make install-mdrun
> 
> Is there anything obviously wrong with those commands?  Is 
> there any way I should know (before actually using mdrun) 
> whether or not I've done things right?

I think there ought to be, but IMO not enough preparation and testing has gone 
into the CMake switch for it to be usable.

Mark
 
> -Justin
> 
> >Roland
> >
> >
> >On Mon, Sep 27, 2010 at 4:59 PM, Justin A. Lemkul 
> mailto:jalem...@vt.edu>> wrote:
> >
> >
> >Hi All,
> >
> >I'm hoping I might get some tips in tracking 
> down the source of an
> >issue that appears to be hardware-specific, 
> leading to crashes in my
> >system.  The failures are occurring on 
> our supercomputer (Mac OSX
> >10.3, PowerPC).  Running the same .tpr 
> file on my laptop (Mac OSX
> >10.5.8, Intel Core2Duo) and on another 
> workstation (Ubuntu 10.04,
> >AMD64) produce identical results.  I 
> suspect the problem stems from
> >unsuccessful energy minimization, which then 
> leads to a crash when
> >running full MD.  All jobs were run in 
> parallel on two cores.  The
> >supercomputer does not support threading, so 
> MPI is invoked using
> >MPICH-1.2.5 (native MPI implementation on 
> the cluster).
> >
> >
> >Details as follows:
> >
> >EM md.log file: successful run (Intel 
> Core2Duo or AMD64)
> >
> >Steepest Descents converged to Fmax < 
> 1000 in 7 steps
> >Potential Energy  = -4.8878180e+04
> >Maximum force 
> =  8.7791553e+02 on atom 5440
> >Norm of force 
> =  1.1781271e+02
> >
> >
> >EM md.log file: unsuccessful run (PowerPC)
> >
> >Steepest Descents converged to Fmax < 
> 1000 in 1 steps
> >Potential Energy  = -2.4873273e+04
> >Maximum force 
> =  0.000e+00 on atom 0
> >Norm of force 
> =nan
> >
> >
> >MD invoked from the minimized structure 
> generated on my laptop or
> >AMD64 runs successfully (at least for a few 
> hundred steps in my
> >test), but the MD on the PowerPC cluster 
> 

Re: [gmx-users] Hardware-specific crash with 4.5.1

[Justin A. Lemkul]

Mark Abraham wrote:



- Original Message -
From: "Justin A. Lemkul" 
Date: Tuesday, September 28, 2010 11:11
Subject: Re: [gmx-users] Hardware-specific crash with 4.5.1
To: Gromacs Users' List 

 >
 >
 > Roland Schulz wrote:
 > >Justin,
 > >
 > >I think the interaction kernel is not OK on your PowerPC
 > machine. I assume that from: 1) The force seems to be zero
 > (minimization output). 2) When you use the all-to-all kernel
 > which is not available for the powerpc kernel, it automatically
 > falls back to the C kernel and then it works.
 > >
 >
 > Sounds about right.
 >
 > >What is the kernel you are using? It should say in the log
 > file. Look for: "Configuring single precision IBM Power6-
 > specific Fortran kernels" or "Testing Altivec/VMX support"
 > >
 >
 > I'm not finding either in the config.log - weird?

You were meant to look in the mdrun.log for runtime confirmation of what 
kernels GROMACS has decided to use.
 


That seems entirely obvious, now that you mention it :)  Conveniently, I find 
the following in the md.log file from the (failing) autoconf-assembled mdrun:


Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing Altivec/VMX support... present.
Configuring PPC/Altivec nonbonded kernels...

The (non)MPI CMake build shows the following:

Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...

So it seems clear to me that autoconf built faulty nonbonded kernels, and CMake 
didn't.



 > >You can also look in the config.h whether  GMX_POWER6
 > and/or GMX_PPC_ALTIVEC is set. I suggest you try to compile with
 > one/both of them deactivated and see whether that solves it.
 > This will make it slower too. Thus if this is indeed the
 > problem, you will probably want to figure out why the fastest
 > kernel doesn't work correctly to get good performance.
 > >
 >
 > It looks like GMX_PPC_ALTIVEC is set.  I suppose I could re-
 > compile with this turned off.

This is supposed to be fine for Mac, as I understand.

 > Here's what's even weirder.  The problematic version was
 > compiled using the standard autoconf procedure.  If I use a
 > CMake-compiled version, the energy minimization runs fine,
 > giving the same results (energy and force) as the two systems I
 > know are good.  So I guess there's something wrong with the
 > way autoconf installed Gromacs.  Perhaps this isn't of
 > concern since Gromacs will require CMake in subsequent releases,
 > but I figure I should at least report it in case it affects
 > anyone else.
 >
 > If I may tack one more question on here, I'm wondering why my
 > CMake installation  doesn't actually appear to be using
 > MPI.  I get the right result, but the problem is, I get a
 > .log, .edr, and .trr for every processor that's being used, as
 > if each processor is being given its own job and not
 > distributing the work. Here's how I compiled my MPI mdrun,
 > version 4.5.1:

At the start and end of the .log files you should get indicators about 
how many MPI processes were actually being used.
 


That explains it (sort of).  It looks like mdrun thinks it's only being run over 
1 node, just several times over, and a bunch of junk that isn't getting written 
properly:


Log file opened on Mon Sep 27 21:36:00 2010
Host: n235  pid: 6857  nodeid: 0  nnodes:  1
The Gromacs distribution was built @TMP_TIME@ by
jalem...@sysx2.arc-int.vt.edu [CMAKE] (@TMP_MACHINE@)

Frustrating.


 > cmake ../gromacs-4.5.1 -DFFTW3F_LIBRARIES=/home/rdiv1001/fftw-
 > 3.0.1-osx/lib/libfftw3f.a -
 > DFFTW3F_INCLUDE_DIR=/home/rdiv1001/fftw-3.0.1-osx/include/ -
 > DCMAKE_INSTALL_PREFIX=/home/rdiv1001/gromacs-4.5_cmake-osx -
 > DGMX_BINARY_SUFFIX=_4.5_cmake_mpi -DGMX_THREADS=OFF -
 > DBUILD_SHARED_LIBS=OFF -DGMX_X11=OFF -DGMX_MPI=ON -
 > DMPI_COMPILER=/home/rdiv1001/compilers/openmpi-1.2.3-
 > osx/bin/mpicxx -
 > DMPI_INCLUDE_PATH=/home/rdiv1001/compilers/openmpi-1.2.3-osx/include
 >
 > $ make mdrun
 >
 > $ make install-mdrun
 >
 > Is there anything obviously wrong with those commands?  Is
 > there any way I should know (before actually using mdrun)
 > whether or not I've done things right?

I think there ought to be, but IMO not enough preparation and testing 
has gone into the CMake switch for it to be usable.




I agree.  After hours of hacking CMake to try to make it work (and thinking I 
had gotten it squared away), the MPI doesn't seem to function.  The "old" way of 
doing things worked flawlessly, except that somewhere between 4.0.7 and 4.5.1, 
the nonbonded kernels that used to work on our architecture somehow got hosed. 
So now I'm in limbo.


-Justin


Mark
 
 > -Justin

 >
 > >Roland
 > >
 > >
 > >On Mon, Sep 27, 2010 at 4:59 PM, Justin A. Lemkul
 > mailto:jalem...@vt.edu>> wrote:
 > >
 > >
 > >Hi All,
 > >
 > >I'm hoping I might get some tips in tracking
 > down the source of an
 > >issue that appears to be hardware-specific,
 > leading to crashes in my
 > >system.  The failures are occurring on
 > o

Re: [gmx-users] Hardware-specific crash with 4.5.1

[Mark Abraham]

- Original Message -
From: "Justin A. Lemkul" 
Date: Tuesday, September 28, 2010 11:39
Subject: Re: [gmx-users] Hardware-specific crash with 4.5.1
To: Discussion list for GROMACS users 

> 
> 
> Mark Abraham wrote:
> >
> >
> >- Original Message -
> >From: "Justin A. Lemkul" 
> >Date: Tuesday, September 28, 2010 11:11
> >Subject: Re: [gmx-users] Hardware-specific crash with 4.5.1
> >To: Gromacs Users' List 
> >
> > >
> > >
> > > Roland Schulz wrote:
> > > >Justin,
> > > >
> > > >I think the interaction kernel is not OK on your PowerPC
> > > machine. I assume that from: 1) The force seems to be zero
> > > (minimization output). 2) When you use the all-to-all kernel
> > > which is not available for the powerpc kernel, it automatically
> > > falls back to the C kernel and then it works.
> > > >
> > >
> > > Sounds about right.
> > >
> > > >What is the kernel you are using? It should say in the log
> > > file. Look for: "Configuring single precision IBM Power6-
> > > specific Fortran kernels" or "Testing Altivec/VMX support"
> > > >
> > >
> > > I'm not finding either in the config.log - weird?
> >
> >You were meant to look in the mdrun.log for runtime 
> confirmation of what kernels GROMACS has decided to use.
> > 
> 
> That seems entirely obvious, now that you mention it :)  
> Conveniently, I find the following in the md.log file from the 
> (failing) autoconf-assembled mdrun:
> 
> Configuring nonbonded kernels...
> Configuring standard C nonbonded kernels...
> Testing Altivec/VMX support... present.
> Configuring PPC/Altivec nonbonded kernels...
> 
> The (non)MPI CMake build shows the following:
> 
> Configuring nonbonded kernels...
> Configuring standard C nonbonded kernels...
> 
> So it seems clear to me that autoconf built faulty nonbonded 
> kernels, and CMake didn't.

OK, so assuming that PPC/Altivec kernels are supposed to be good for Mac (as 
they were in 4.0.x, I believe):

1) CMake doesn't detect that it should be using those kernels, and so appears 
to work, but does an inefficient run. autoconf detects that it should use those 
kernels, but the mdrun fails for reasons that are not yet clear.
 
> > > >You can also look in the config.h whether  GMX_POWER6
> > > and/or GMX_PPC_ALTIVEC is set. I suggest you try to compile with
> > > one/both of them deactivated and see whether that solves it.
> > > This will make it slower too. Thus if this is indeed the
> > > problem, you will probably want to figure out why the fastest
> > > kernel doesn't work correctly to get good performance.
> > > >
> > >
> > > It looks like GMX_PPC_ALTIVEC is set.  I suppose I 
> could re-
> > > compile with this turned off.
> >
> >This is supposed to be fine for Mac, as I understand.
> >
> > > Here's what's even weirder.  The problematic version was
> > > compiled using the standard autoconf procedure.  If I 
> use a
> > > CMake-compiled version, the energy minimization runs fine,
> > > giving the same results (energy and force) as the two 
> systems I
> > > know are good.  So I guess there's something wrong with the
> > > way autoconf installed Gromacs.  Perhaps this isn't of
> > > concern since Gromacs will require CMake in subsequent releases,
> > > but I figure I should at least report it in case it affects
> > > anyone else.
> > >
> > > If I may tack one more question on here, I'm wondering why my
> > > CMake installation  doesn't actually appear to be using
> > > MPI.  I get the right result, but the problem is, I get a
> > > .log, .edr, and .trr for every processor that's being used, as
> > > if each processor is being given its own job and not
> > > distributing the work. Here's how I compiled my MPI mdrun,
> > > version 4.5.1:
> >
> >At the start and end of the .log files you should get 
> indicators about how many MPI processes were actually being used.
> > 
> 
> That explains it (sort of).  It looks like mdrun thinks 
> it's only being run over 1 node, just several times over, and a 
> bunch of junk that isn't getting written properly:
> 
> Log file opened on Mon Sep 27 21:36:00 2010
> Host: n235  pid: 6857  nodeid: 0  nnodes:  1
> The Gromacs distribution was built @TMP_TIME@ by
> jalem...@sysx2.arc-int.vt.edu [CMAKE] (@TMP_MACHINE@)
> 
> Frustrating.

You can set the GMX_NOOPTIMIZEDKERNELS environment variable with your autoconf 
build to see whether the MPI issue is CMake-dependent. Normally, I'd say your 
supercomputer MPI environment isn't being invoked correctly, but presumably you 
already know how to do that right...

> > > cmake ../gromacs-4.5.1 -
> DFFTW3F_LIBRARIES=/home/rdiv1001/fftw-
> > > 3.0.1-osx/lib/libfftw3f.a -
> > > DFFTW3F_INCLUDE_DIR=/home/rdiv1001/fftw-3.0.1-osx/include/ -
> > > DCMAKE_INSTALL_PREFIX=/home/rdiv1001/gromacs-4.5_cmake-osx -
> > > DGMX_BINARY_SUFFIX=_4.5_cmake_mpi -DGMX_THREADS=OFF -
> > > DBUILD_SHARED_LIBS=OFF -DGMX_X11=OFF -DGMX_MPI=ON -
> > > DMPI_COMPILER=/home/rdiv1001/compilers/openmpi-1.2.3-
> > > osx/bin/mpicxx -
> > > DMPI_INCLUDE_PATH=/home/rdiv1001/co

RE: [gmx-users] How to make a lipid bilayer with specific dimensions?

[NG HUI WEN]

Thanks for that guys! I will try them out.

Just a quick question here with regards to my lipids being possibly too
small,  does it have something to do with the minimum image criterion
for PBC? I have ensured that the distance of edge of the box and the
atoms at the side of the protein to be greater than the cutoff of 1.2nm
(PME is used)... in the hope that the protein would not interact with
it's neighbouring image. I hope I'm not going down the wrong direction
in my understanding of pbc...

Thanks!!!

-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of
chris.ne...@utoronto.ca
Sent: Monday, September 27, 2010 8:30 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] How to make a lipid bilayer with specific
dimensions?

I don't think that this is currently causing anybody any problems, but  
note that genbox is going to cut any lipids that cross out of the  
central unit box (either because genbox is unaware of PBC or because  
these lipids now clash across PBC).

Therefore:

genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919

will give you a bilayer that gets solvated with a water defect around  
the edges of the initial unit cell and that, after 10 - 200 ns of  
simulation, gives you an equilibrated bilayer (without water defect)  
that is much smaller than x=9.6, y=9.5.

To get what you want, you need to either start your bilayer with  
larger x and y (calculate area per lipid in 9.6*9.5 to figure out how  
many lipids you should have and keep running genbox until you get  
that), or perhaps a run through inflategro might do it.

Chris.
  --original message --

[gmx-users] How to make a lipid bilayer with specific dimensions?
Justin A. Lemkul jalemkul at vt.edu
Mon Sep 27 13:00:32 CEST 2010

 * Previous message: [gmx-users] How to make a lipid bilayer with  
specific dimensions?
 * Next message: [gmx-users] Query regarding protonation and  
deprotonation of some residues
 * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

NG HUI WEN wrote:
> Dear gmxusers,
>
>  I am trying to make a lipid bilayer with specific dimensions using  
> gromacs. So far, I have got up to:
>
>  1)  Download a lipid POPC128a.pdb from Peter Tieleman?s website
>
> 2)  Use genconf ?f popc128a.pdb ?o popcx2.pdb ?nbox 2   2   1 to  
> multiply the lipid in the x and y axis. The resultant output was a  
> lipid with box vectors 12.478 ,   12.359 and 6.919 (nm)
>
>  My ultimate aim is to generate a POPC bilayer with the dimensions  
> 9.600   9.500 and 14.000. Currently, the lipid bilayer is too big. I

Too big?  If you're using either of the two coordinate files above
(popc128a.pdb, popcx2.pdb), they should be too small.

> would like to ?crop? the excess lipids to the required size if at  
> all possible. I tried using editconf ( a bit of a long shot) to make  
> a new box size. The new structure file has a CRYST1 of 9.600   9.500  
> and 14.000 but when I view it with VMD, it is not any smaller than  
> before.
>
>  Do I have to use other software to achieve this? If so, I?d really  
> appreciate some pointers.
>

You can do this in three steps.  If your goal is to have a single  
lipid bilayer
in the middle of the box, with water around it:

genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919
editconf -f popc_new.pdb -o popc_new2.pdb -c -box 9.6 9.5 14
genbox -cp popc_new2.pdb -cs spc216.gro -o solv.pdb

The reason you need three steps is that if you supply a z-dimension of  
14 in the
first genbox command, at least two full bilayers (or some fraction  
close to it)
will be placed in your box.  If that's your goal, then this can be  
done in one step.

-Justin
>  Thanks!
>
> <<
>
> Email has been scanned for viruses by UNMC email management service  
> 
>
>  >>
>

-- 


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



 * Previous message: [gmx-users] How to make a lipid bilayer with  
specific dimensions?
 * Next message: [gmx-users] Query regarding protonation and  
deprotonation of some residues
 * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

More information about the gmx-users mailing list


-- 
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!
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
<< Email has been scanned for viruses by UNMC email management service
>>
<< Email has been scanned for viruses by UNMC email management 

Re: [gmx-users] How to make a lipid bilayer with specific dimensions?

[Justin A. Lemkul]

NG HUI WEN wrote:

Thanks for that guys! I will try them out.

Just a quick question here with regards to my lipids being possibly too
small,  does it have something to do with the minimum image criterion
for PBC? I have ensured that the distance of edge of the box and the
atoms at the side of the protein to be greater than the cutoff of 1.2nm
(PME is used)... in the hope that the protein would not interact with
it's neighbouring image. I hope I'm not going down the wrong direction
in my understanding of pbc...

Thanks!!!



There is no direct relationship between genbox and the minimum image convention. 
 You certainly need to build a system that is of sufficient size to avoid 
spurious PBC interactions, but when genbox does is independent of this fact. 
The problem is that genbox will not place a molecule that falls partially 
outside the box, thus deleting an entire lipid and leaving a gap at the edge of 
the box.  Like Chris said, this can lead to your system compressing somewhat to 
give dimensions smaller than what you were hoping for.  Whether or not this is a 
problem in the long run is up to you to decide based on the specifics of your 
system.


Short answer: make your box slightly larger than you think you need and 
equilibrate for a long time to ensure that your box is stable.


-Justin


-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of
chris.ne...@utoronto.ca
Sent: Monday, September 27, 2010 8:30 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] How to make a lipid bilayer with specific
dimensions?

I don't think that this is currently causing anybody any problems, but  
note that genbox is going to cut any lipids that cross out of the  
central unit box (either because genbox is unaware of PBC or because  
these lipids now clash across PBC).


Therefore:

genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919

will give you a bilayer that gets solvated with a water defect around  
the edges of the initial unit cell and that, after 10 - 200 ns of  
simulation, gives you an equilibrated bilayer (without water defect)  
that is much smaller than x=9.6, y=9.5.


To get what you want, you need to either start your bilayer with  
larger x and y (calculate area per lipid in 9.6*9.5 to figure out how  
many lipids you should have and keep running genbox until you get  
that), or perhaps a run through inflategro might do it.


Chris.
  --original message --

[gmx-users] How to make a lipid bilayer with specific dimensions?
Justin A. Lemkul jalemkul at vt.edu
Mon Sep 27 13:00:32 CEST 2010

 * Previous message: [gmx-users] How to make a lipid bilayer with  
specific dimensions?
 * Next message: [gmx-users] Query regarding protonation and  
deprotonation of some residues

 * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

NG HUI WEN wrote:

Dear gmxusers,

 I am trying to make a lipid bilayer with specific dimensions using  
gromacs. So far, I have got up to:


 1)  Download a lipid POPC128a.pdb from Peter Tieleman?s website

2)  Use genconf ?f popc128a.pdb ?o popcx2.pdb ?nbox 2   2   1 to  
multiply the lipid in the x and y axis. The resultant output was a  
lipid with box vectors 12.478 ,   12.359 and 6.919 (nm)


 My ultimate aim is to generate a POPC bilayer with the dimensions  
9.600   9.500 and 14.000. Currently, the lipid bilayer is too big. I


Too big?  If you're using either of the two coordinate files above
(popc128a.pdb, popcx2.pdb), they should be too small.

would like to ?crop? the excess lipids to the required size if at  
all possible. I tried using editconf ( a bit of a long shot) to make  
a new box size. The new structure file has a CRYST1 of 9.600   9.500  
and 14.000 but when I view it with VMD, it is not any smaller than  
before.


 Do I have to use other software to achieve this? If so, I?d really  
appreciate some pointers.




You can do this in three steps.  If your goal is to have a single  
lipid bilayer

in the middle of the box, with water around it:

genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919
editconf -f popc_new.pdb -o popc_new2.pdb -c -box 9.6 9.5 14
genbox -cp popc_new2.pdb -cs spc216.gro -o solv.pdb

The reason you need three steps is that if you supply a z-dimension of  
14 in the
first genbox command, at least two full bilayers (or some fraction  
close to it)
will be placed in your box.  If that's your goal, then this can be  
done in one step.


-Justin

 Thanks!

<<

Email has been scanned for viruses by UNMC email management service  



 >>





--


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:/

RE: [gmx-users] How to make a lipid bilayer with specific dimensions?

[NG HUI WEN]

Points noted, thanks Justin!

-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
Sent: Tuesday, September 28, 2010 10:06 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to make a lipid bilayer with specific
dimensions?



NG HUI WEN wrote:
> Thanks for that guys! I will try them out.
> 
> Just a quick question here with regards to my lipids being possibly
too
> small,  does it have something to do with the minimum image criterion
> for PBC? I have ensured that the distance of edge of the box and the
> atoms at the side of the protein to be greater than the cutoff of
1.2nm
> (PME is used)... in the hope that the protein would not interact with
> it's neighbouring image. I hope I'm not going down the wrong direction
> in my understanding of pbc...
> 
> Thanks!!!
> 

There is no direct relationship between genbox and the minimum image
convention. 
  You certainly need to build a system that is of sufficient size to
avoid 
spurious PBC interactions, but when genbox does is independent of this
fact. 
The problem is that genbox will not place a molecule that falls
partially 
outside the box, thus deleting an entire lipid and leaving a gap at the
edge of 
the box.  Like Chris said, this can lead to your system compressing
somewhat to 
give dimensions smaller than what you were hoping for.  Whether or not
this is a 
problem in the long run is up to you to decide based on the specifics of
your 
system.

Short answer: make your box slightly larger than you think you need and 
equilibrate for a long time to ensure that your box is stable.

-Justin

> -Original Message-
> From: gmx-users-boun...@gromacs.org
> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of
> chris.ne...@utoronto.ca
> Sent: Monday, September 27, 2010 8:30 PM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] How to make a lipid bilayer with specific
> dimensions?
> 
> I don't think that this is currently causing anybody any problems, but

> note that genbox is going to cut any lipids that cross out of the  
> central unit box (either because genbox is unaware of PBC or because  
> these lipids now clash across PBC).
> 
> Therefore:
> 
> genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919
> 
> will give you a bilayer that gets solvated with a water defect around

> the edges of the initial unit cell and that, after 10 - 200 ns of  
> simulation, gives you an equilibrated bilayer (without water defect)  
> that is much smaller than x=9.6, y=9.5.
> 
> To get what you want, you need to either start your bilayer with  
> larger x and y (calculate area per lipid in 9.6*9.5 to figure out how

> many lipids you should have and keep running genbox until you get  
> that), or perhaps a run through inflategro might do it.
> 
> Chris.
>   --original message --
> 
> [gmx-users] How to make a lipid bilayer with specific dimensions?
> Justin A. Lemkul jalemkul at vt.edu
> Mon Sep 27 13:00:32 CEST 2010
> 
>  * Previous message: [gmx-users] How to make a lipid bilayer with

> specific dimensions?
>  * Next message: [gmx-users] Query regarding protonation and  
> deprotonation of some residues
>  * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
> 
> NG HUI WEN wrote:
>> Dear gmxusers,
>>
>>  I am trying to make a lipid bilayer with specific dimensions using  
>> gromacs. So far, I have got up to:
>>
>>  1)  Download a lipid POPC128a.pdb from Peter Tieleman?s website
>>
>> 2)  Use genconf ?f popc128a.pdb ?o popcx2.pdb ?nbox 2   2   1 to

>> multiply the lipid in the x and y axis. The resultant output was a  
>> lipid with box vectors 12.478 ,   12.359 and 6.919 (nm)
>>
>>  My ultimate aim is to generate a POPC bilayer with the dimensions  
>> 9.600   9.500 and 14.000. Currently, the lipid bilayer is too big. I
> 
> Too big?  If you're using either of the two coordinate files above
> (popc128a.pdb, popcx2.pdb), they should be too small.
> 
>> would like to ?crop? the excess lipids to the required size if at  
>> all possible. I tried using editconf ( a bit of a long shot) to make

>> a new box size. The new structure file has a CRYST1 of 9.600   9.500

>> and 14.000 but when I view it with VMD, it is not any smaller than  
>> before.
>>
>>  Do I have to use other software to achieve this? If so, I?d really  
>> appreciate some pointers.
>>
> 
> You can do this in three steps.  If your goal is to have a single  
> lipid bilayer
> in the middle of the box, with water around it:
> 
> genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919
> editconf -f popc_new.pdb -o popc_new2.pdb -c -box 9.6 9.5 14
> genbox -cp popc_new2.pdb -cs spc216.gro -o solv.pdb
> 
> The reason you need three steps is that if you supply a z-dimension of

> 14 in the
> first genbox command, at least two full bilayers (or some fraction  
> close to it)
> will be placed in your box.  If that's your goal, then this can be  
> done in one step.
> 

[gmx-users] Compilation error - GROMACS 4.5.1

[Shachi Katira]

Hi all,

I get the following errors when I try to compile the double precision
version of GROMACS 4.5.1 using:

./configure --prefix=/home/shachi/gromacs --enable-double
--with-fft=fft3 --without-x

Errors:

In file included from nb_kernel400_x86_64_sse2.c:24:
../../../../include/gmx_sse2_double.h: In function `gmx_mm_sincos_pd':
../../../../include/gmx_sse2_double.h:457: warning: implicit
declaration of function `_mm_castsi128_pd'
../../../../include/gmx_sse2_double.h:457: error: invalid initializer
../../../../include/gmx_sse2_double.h:514: error: incompatible type
for argument 1 of `_mm_and_pd'
../../../../include/gmx_sse2_double.h:515: error: incompatible type
for argument 1 of `_mm_andnot_pd'
../../../../include/gmx_sse2_double.h:516: error: incompatible type
for argument 1 of `_mm_and_pd'
../../../../include/gmx_sse2_double.h:517: error: incompatible type
for argument 1 of `_mm_andnot_pd'

A similar query was posted two weeks ago
(http://lists.gromacs.org/pipermail/gmx-users/2010-September/053984.html).
I'm having the same problem in spite of using gcc 4.4.4.

I'm using CentOS 4, gcc 4.4.4 on an AMD Opteron 285 (x86_64). The FFTW
version I'm using is 3.2.2.

It, however, compiles fine on an Intel Xeon 5462 (IA32) machine
running MacOS 10.5, gcc 4.4.4.

Thanks.

-Shachi
-- 
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!
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

Re: [gmx-users] Compilation error - GROMACS 4.5.1

[Mark Abraham]

- Original Message -
From: Shachi Katira 
Date: Tuesday, September 28, 2010 12:56
Subject: [gmx-users] Compilation error - GROMACS 4.5.1
To: gmx-users@gromacs.org

> Hi all,
> 
> I get the following errors when I try to compile the double precision
> version of GROMACS 4.5.1 using:
  > 
> ./configure --prefix=/home/shachi/gromacs --enable-double
> --with-fft=fft3 --without-x

You need "--with-fft=fftw3".

> Errors:
> 
> In file included from nb_kernel400_x86_64_sse2.c:24:
> ../../../../include/gmx_sse2_double.h: In function `gmx_mm_sincos_pd':
>   ../../../../include/gmx_sse2_double.h:457: warning: implicit
> declaration of function `_mm_castsi128_pd'
> ../../../../include/gmx_sse2_double.h:457: error: invalid initializer
> ../../../../include/gmx_sse2_double.h:514: error: incompatible type
>   for argument 1 of `_mm_and_pd'
> ../../../../include/gmx_sse2_double.h:515: error: incompatible type
> for argument 1 of `_mm_andnot_pd'
> ../../../../include/gmx_sse2_double.h:516: error: incompatible type
>   for argument 1 of `_mm_and_pd'
> ../../../../include/gmx_sse2_double.h:517: error: incompatible type
> for argument 1 of `_mm_andnot_pd'
> 
> A similar query was posted two weeks ago
> (http://lists.gromacs.org/pipermail/gmx-users/2010-September/053984.html).
>   I'm having the same problem in spite of using gcc 4.4.4.
> 
> I'm using CentOS 4, gcc 4.4.4 on an AMD Opteron 285 (x86_64). The FFTW
> version I'm using is 3.2.2.
> 
> It, however, compiles fine on an Intel Xeon 5462 (IA32) machine
>   running MacOS 10.5, gcc 4.4.4.

Check out the output of configure to see what compiler it thinks it is using.

Mark

-- 
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!
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

Re: [gmx-users] Hardware-specific crash with 4.5.1

[Roland Schulz]

On Mon, Sep 27, 2010 at 9:58 PM, Mark Abraham wrote:

>
>
> - Original Message -
> From: "Justin A. Lemkul" 
> Date: Tuesday, September 28, 2010 11:39
> Subject: Re: [gmx-users] Hardware-specific crash with 4.5.1
> To: Discussion list for GROMACS users 
>
> >
> >
> > Mark Abraham wrote:
> > >
> > >
> > >- Original Message -
> > >From: "Justin A. Lemkul" 
> > >Date: Tuesday, September 28, 2010 11:11
> > >Subject: Re: [gmx-users] Hardware-specific crash with 4.5.1
> > >To: Gromacs Users' List 
> > >
> > > >
> > > >
> > > > Roland Schulz wrote:
> > > > >Justin,
> > > > >
> > > > >I think the interaction kernel is not OK on your PowerPC
> > > > machine. I assume that from: 1) The force seems to be zero
> > > > (minimization output). 2) When you use the all-to-all kernel
> > > > which is not available for the powerpc kernel, it automatically
> > > > falls back to the C kernel and then it works.
> > > > >
> > > >
> > > > Sounds about right.
> > > >
> > > > >What is the kernel you are using? It should say in the log
> > > > file. Look for: "Configuring single precision IBM Power6-
> > > > specific Fortran kernels" or "Testing Altivec/VMX support"
> > > > >
> > > >
> > > > I'm not finding either in the config.log - weird?
> > >
> > >You were meant to look in the mdrun.log for runtime
> > confirmation of what kernels GROMACS has decided to use.
> > >
> >
> > That seems entirely obvious, now that you mention it :)
> > Conveniently, I find the following in the md.log file from the
> > (failing) autoconf-assembled mdrun:
> >
> > Configuring nonbonded kernels...
> > Configuring standard C nonbonded kernels...
> > Testing Altivec/VMX support... present.
> > Configuring PPC/Altivec nonbonded kernels...
> >
> > The (non)MPI CMake build shows the following:
> >
> > Configuring nonbonded kernels...
> > Configuring standard C nonbonded kernels...
> >
> > So it seems clear to me that autoconf built faulty nonbonded
> > kernels, and CMake didn't.
>
> OK, so assuming that PPC/Altivec kernels are supposed to be good for Mac
> (as they were in 4.0.x, I believe):
>
> 1) CMake doesn't detect that it should be using those kernels, and so
> appears to work, but does an inefficient run. autoconf detects that it
> should use those kernels, but the mdrun fails for reasons that are not yet
> clear.
>
>
> > > > >You can also look in the config.h whether  GMX_POWER6
> > > > and/or GMX_PPC_ALTIVEC is set. I suggest you try to compile with
> > > > one/both of them deactivated and see whether that solves it.
> > > > This will make it slower too. Thus if this is indeed the
> > > > problem, you will probably want to figure out why the fastest
> > > > kernel doesn't work correctly to get good performance.
> > > > >
> > > >
> > > > It looks like GMX_PPC_ALTIVEC is set.  I suppose I
> > could re-
> > > > compile with this turned off.
> > >
> > >This is supposed to be fine for Mac, as I understand.
> > >
> > > > Here's what's even weirder.  The problematic version was
> > > > compiled using the standard autoconf procedure.  If I
> > use a
> > > > CMake-compiled version, the energy minimization runs fine,
> > > > giving the same results (energy and force) as the two
> > systems I
> > > > know are good.  So I guess there's something wrong with the
> > > > way autoconf installed Gromacs.  Perhaps this isn't of
> > > > concern since Gromacs will require CMake in subsequent releases,
> > > > but I figure I should at least report it in case it affects
> > > > anyone else.
> > > >
> > > > If I may tack one more question on here, I'm wondering why my
> > > > CMake installation  doesn't actually appear to be using
> > > > MPI.  I get the right result, but the problem is, I get a
> > > > .log, .edr, and .trr for every processor that's being used, as
> > > > if each processor is being given its own job and not
> > > > distributing the work. Here's how I compiled my MPI mdrun,
> > > > version 4.5.1:
> > >
> > >At the start and end of the .log files you should get
> > indicators about how many MPI processes were actually being used.
> > >
> >
> > That explains it (sort of).  It looks like mdrun thinks
> > it's only being run over 1 node, just several times over, and a
> > bunch of junk that isn't getting written properly:
> >
> > Log file opened on Mon Sep 27 21:36:00 2010
> > Host: n235  pid: 6857  nodeid: 0  nnodes:  1
> > The Gromacs distribution was built @TMP_TIME@ by
> > jalem...@sysx2.arc-int.vt.edu [CMAKE] (@TMP_MACHINE@)
> >
> > Frustrating.
>
> You can set the GMX_NOOPTIMIZEDKERNELS environment variable with your
> autoconf build to see whether the MPI issue is CMake-dependent. Normally,
> I'd say your supercomputer MPI environment isn't being invoked correctly,
> but presumably you already know how to do that right...
>
>
> > > > cmake ../gromacs-4.5.1 -
> > DFFTW3F_LIBRARIES=/home/rdiv1001/fftw-
> > > > 3.0.1-osx/lib/libfftw3f.a -
> > > > DFFTW3F_INCLUDE_DIR=/home/rdiv1001/fftw-3.0.1-osx/include/ -
> > > > DCMAKE_INSTALL_PREFIX=/home