[gmx-users] Question about biphasic tutorial

[James Lord]

Hi all,
I want to make the the hydrophobic layer Justin has made but only have one
.itp file from ATB for the hydrophobic layer (no topology and coordinate)?
Any suggestion where and how to start to make this  hydrophobic layer? I am
aware of what Justin has suggested regarding using PRODRG
,. any comments?
Cheers
James
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[gmx-users] Chlorine in PDBs

[az]

Hi

Could someone enlighten me what are the "correct" (Gromacs-wise) atom 
type and PDB column numbers for a chlorine substituent in a ligand ? I 
use a MOE-written PDBs as MD input (Amber99SB), and if a chlorine is 
present, its written as CL (both letters uppercase) in the 13th and 14th 
column. Now when feeding that to acpype, the output PDB has a CL again, 
but shifted to columns 14 and 15 and with a C in the last element 
column. Seeing how this is similar to how box ions are written, I gave 
it no heed, but now PDBs saved from a completed trajectory, display the 
CL as a carbon in VMD, Chimera, or MOE. I can obviously edit that but 
I'd like to be sure if my CLs are being treated as chlorines during the MD.


Input line:HETATM 2166 CL   PXN 0  -7.547  -4.598 6.977  
1.00  0.00  CL
Post-acpype:ATOM 26  CL  PXN Z   1  -7.547  -4.598 6.977  
1.00  0.00   C
Post-MD:ATOM   2147  CL  PXN B 169   2.196   0.709 5.879  
1.002409.13


Cheers,
Adam
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Re: [gmx-users] Best step to run simulation over GPU?

[Kutzner, Carsten]

Hi,

> On 24 Jul 2015, at 08:48, RJ  wrote:
> 
> Dear gmx,
> 
> 
> I have a single PC contains 24 threads with GTX 980Ti.
> 
> 
> I would like to know how do i run the 3 or 2 simulation in same time with 
> above mentioned PC would have similar speed.
Simply try it out :)

It could be beneficial to use the -multi options of gmx mdrun
to start the multiple simulations. This way GROMACS would automatically
take care of proper process placement and pinning.

You could make a quick check with, e.g., mdrun -nsteps 5000 -resethway -multi …
to get a performance estimate for 2 and for 3 simulations.

There is more information about this on page 7 of
http://arxiv.org/src/1507.00898v1/anc/supporting.pdf

Carsten


> I also read about -pin options but couldnt understand well. Moreover i run in 
> default i get this error "The GPU has >25% less load than the CPU. This 
> imbalance causes performance loss".
> 
> 
> Its much appreciated if you could provide some info about multi simulation. 
> Thanks.
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

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Re: [gmx-users] Enforced rotation errors

[Kutzner, Carsten]

Hi Anthony,

> On 24 Jul 2015, at 01:56, Nash, Anthony  wrote:
> 
> After going through the literature, I think my problem lies with not
> having defined a pivot point and using what was original defined in the
> developer’s .mdp file example.
> 
> I understand what a pivot point is, but I am not sure how to calculate it.
> Any suggestions would be great.
If you want the rotation group to rotate about its own axis, then use
the center of mass as the pivot, which g_traj can calculate, e.g.
The pivot will have an effect in the iso, but not in the flex potentials, 
though.

Carsten


> 
> Thanks
> Anthony
> 
> 
> 
> On 24/07/2015 00:16, "Nash, Anthony"  wrote:
> 
>> Dear Carsten,
>> 
>> Thanks for that suggestion. Seems like that solved that particular
>> problem. Unfortunately though, my trajectory is not what I expected.
>> 
>> I have been able to rotate the cylindrical ligand about it¹s principle
>> axis in an earlier Œprototype¹ of my enzyme-ligand complex using iso-pf
>> enforced rotation. But after replacing the ligand with the Œreal¹ thing
>> and running a regular MD simulation for 200ns, I¹ve failed to recreate the
>> desired rotation using enforced rotation. I original started with iso-pf
>> (as it worked in the earlier case), but this resulted in lots of LINCS
>> errors. I then tried flex (as per my original post) and now flex-t.
>> 
>> I begin by calculating the moment of inertia of my cylindrical enzyme.
>> Using the lal01psx script for VMD I pick the 3rd vector which I add to the
>> .mdp file as:
>> 
>> rot-vec0 = 0.691585601358247 -0.6995947474399045 0.17965674311989613
>> 
>> It looks as though the ligand is being rotated in a big arch, rather than
>> rotated around its length/long axis. I take it enforced rotation, applies
>> the potential about this vector? My inputs are:
>> 
>> ; ENFORCED ROTATION
>> ; Enforced rotation: No or Yes
>> rotation = Yes
>> ; Output frequency for angle, torque and rotation potential energy for the
>> whole group
>> rot-nstrout  = 1
>> ; Output frequency for per-slab data (angles, torques and slab centers)
>> rot-nstsout  = 10
>> ; Number of rotation groups
>> rot-ngroups  = 1
>> ; Rotation group name
>> rot-group0   = Collagen_CA
>> ; Rotation potential. Can be iso, iso-pf, pm, pm-pf, rm, rm-pf, rm2,
>> rm2-pf, flex, flex-t, flex2, flex2-t
>> rot-type0= flex-t ;iso-pf ;using a pivot free i.e., a
>> detached!:
>> ; Use mass-weighting of the rotation group positions
>> rot-massw0   = yes
>> ; Rotation vector, will get normalized
>> rot-vec0 = 0.691585601358247 -0.6995947474399045 0.17965674311989613
>> 
>> 
>> ; Pivot point for the potentials iso, pm, rm, and rm2 [nm]
>> ;rot-pivot0   = 4.31852e+00  1.73201e+00  1.89800e+00
>> 
>> 
>> ; Rotation rate [degree/ps] and force constant [kJ/(mol*nm^2)]
>> rot-rate0= 0.021  ;
>> rot-k0   = 600.0 ; <- change 100 through to 600
>> ; Slab distance for flexible axis rotation [nm]
>> rot-slab-dist0   = 1
>> ; Minimum value of Gaussian function for the force to be evaluated (for
>> flex* potentials)
>> rot-min-gauss0   = 0.001
>> ; Value of additive constant epsilon' [nm^2] for rm2* and flex2*
>> potentials
>> rot-eps0 = 0.0001
>> ; Fitting method to determine angle of rotation group (rmsd, norm, or
>> potential)
>> rot-fit-method0  = norm
>> ; For fit type 'potential', nr. of angles around the reference for which
>> the pot. is evaluated
>> rot-potfit-nsteps0   = 21
>> ; For fit type 'potential', distance in degrees between two consecutive
>> angles
>> rot-potfit-step0 = 0.25
>> 
>> Any suggestions are gratefully appreciated.
>> 
>> Thanks
>> Anthony
>> 
>> Dr Anthony Nash
>> Department of Chemistry
>> University College London
>> 
>> 
>> 
>> 
>> 
>> On 20/07/2015 15:53, "Kutzner, Carsten"  wrote:
>> 
>>> Dear Anthony,
>>> 
>>> the problem you are experiencing with the Œflex¹ rotation potential
>>> could be related to the rotation group moving too far along the direction
>>> of the rotation vector. As for V_flex, the slabs are fixed in space,
>>> the rotation group may after some time enter a region where no reference
>>> slab centers are defined, triggering the error that you see.
>>> 
>>> In that case, you can use the Œflex-t¹ variant of the potential. Here,
>>> the midplane of slab n=0 is attached to the center of mass of the
>>> rotation group, so that the slabs move with the rotation group.
>>> See equations 6.46 and 6.47 in the GROMACS 5.0 PDF manual.
>>> 
>>> Carsten
>>> 
>>> 
 On 20 Jul 2015, at 16:20, Nash, Anthony  wrote:
 
 Dear All,
 
 I hope you can help. I am using 'flex' enforced rotation to rotate a
 cylindrical protein along the surface of a globular protein.
 Unfortunately my system is experiencing what I can only assume is an IO
 problem:
 
 DD  step 94 load imb.: force  2.9%  pme 

Re: [gmx-users] itp file not found

[su]

Dear James 
I think you din't give Justin a chance to reply 😉 I mean you solved your query 
yourself. Rather, i was waiting for Mark's sarcastic comment 😀😀 Well, i had the 
same problem but like you, it was solved. 
Best Regards
Suniba

Sent from my iPhone

> On 24-Jul-2015, at 7:05 am, James Lord  wrote:
> 
> Hi All,
> Problem solved.
> http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx
> 
> Am I the only one missing Justin and his lovely comments??
> Cheers
> James
> 
> On Wed, Jul 22, 2015 at 11:11 PM, James Lord 
> wrote:
> 
>> Hi all,
>> I am running energy minimization and grompp is complaining about following
>> error. I am using Gromacs version 4.6.3. On Gromacs website it is saying
>> that GROMOS96 54A7 files from ATB website  were added to 4.6.2 and later
>> versions right?
>> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x
>> 
>> 
>>  Program grompp, VERSION 4.6.3
>> Source code file: /home/James/gromacs-4.6.3/src/gmxlib/gmxcpp.c, line: 293
>> 
>> Fatal error:
>> Topology include file "ffG54a7.itp" not found
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> 
>> My first question is why this .itp file can't be located by grompp?
>> 
>> I tried to bypass it and downloaded the gromos54a7.ff from ATB (
>> GROMOS_54A7_for_Gromacs_4.5.x_5.x.x.tar.gz
>> 
>> )
>> and extracted the force field  and put it in my working directory. but
>> again grompp is not happy??!!
>> 
>> Program grompp, VERSION 4.6.3
>> Source code file: /home/James/gromacs-4.6.3/src/kernel/topio.c, line: 734
>> 
>> Fatal error:
>> Syntax error - File forcefield.itp, line 4
>> Last line read:
>> '[ defaults ]'
>> Invalid order for directive defaults
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> 
>> the topology file and the included "decane_G54A7.itp" file in line 4 are
>> uploaded. Any thought would be greatly appreciated.
>> https://drive.google.com/file/d/0B0YMTXH1gmQscndZcVJxZnZGU2M/view?usp=sharing
>> https://drive.google.com/file/d/0B0YMTXH1gmQsVGV0WXBSMU1GbFU/view?usp=sharing
>> Cheers
>> James
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Re: [gmx-users] multi threads pinning problem

[terrencesun]

Hi,

The -pin is used to prevent the OS switching threads across physical cores, 
which may result in performance loss. If you want to pin your threads to cores, 
use -pin on. -pinoffset can help you set to which cores your threads are 
pinned, which is stated in mdrun -h.

Regards
Terry


> On 24 Jul 2015, at 11:53 am, Zhenyu Meng  wrote:
> 
> Dear all,
> When I'm running gromacs with mdrun, I always receive such message:
> 
> The number of threads is not equal to the number of (logical) cores
> and the -pin option is set to auto: will not pin thread to cores.
> This can lead to significant performance degradation.
> Consider using -pin on (and -pinoffset in case you run multiple jobs).
> 
> The server I use has 128 cores, and usually I use mdrun with flag -nt 32 or
> -nt 64 to specify the threads, I also notice there's large performance lost
> in each run.
> I wonder what's the difference between '-pin on' and '-pinoffset'. I
> usually run multi jobs on the server so will '-pin on' or '-pinoffset'
> affect the other jobs? If I use '-pinoffset' what value I should
> set(suppose I have already use 32 cores for other jobs)?
> 
> -- 
> Sincerely,
> Mr. Meng Zhenyu
> Division of Chemistry and Biological Chemistry
> School of Physical and Mathematical Sciences
> Nanyang Technological University
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[gmx-users] GTP and GTP topology for OPLS-AA force field

[Christian Bope Domilongo]

Dear All,

I want to generate topology file for Guanosine-5'-triphosphate (GTP) and
Guanosine diphosphate (GDP) for   OPLS-AA force field in order to run mmy
simulation Groamcs.

Any suggestion.

Thank you
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Re: [gmx-users] multi threads pinning problem

[Mark Abraham]

Hi,

Check out
http://manual.gromacs.org/documentation/5.1-rc1/user-guide/mdrun-performance.html
and
http://manual.gromacs.org/documentation/5.1-rc1/user-guide/mdrun-features.html#running-multi-simulations.
It's hard to be definitive about the correct thing to do, since it depends
very much on all of your infrastructure. You should observe the performance
when using all the cores (pinned by default) and when using a single
(pinned) core and expect performance to be reasonable consistent as you
change the number of cores.

Mark

On Fri, Jul 24, 2015 at 12:18 PM  wrote:

> Hi,
>
> The -pin is used to prevent the OS switching threads across physical
> cores, which may result in performance loss. If you want to pin your
> threads to cores, use -pin on. -pinoffset can help you set to which cores
> your threads are pinned, which is stated in mdrun -h.
>
> Regards
> Terry
>
>
> > On 24 Jul 2015, at 11:53 am, Zhenyu Meng  wrote:
> >
> > Dear all,
> > When I'm running gromacs with mdrun, I always receive such message:
> >
> > The number of threads is not equal to the number of (logical) cores
> > and the -pin option is set to auto: will not pin thread to cores.
> > This can lead to significant performance degradation.
> > Consider using -pin on (and -pinoffset in case you run multiple jobs).
> >
> > The server I use has 128 cores, and usually I use mdrun with flag -nt 32
> or
> > -nt 64 to specify the threads, I also notice there's large performance
> lost
> > in each run.
> > I wonder what's the difference between '-pin on' and '-pinoffset'. I
> > usually run multi jobs on the server so will '-pin on' or '-pinoffset'
> > affect the other jobs? If I use '-pinoffset' what value I should
> > set(suppose I have already use 32 cores for other jobs)?
> >
> > --
> > Sincerely,
> > Mr. Meng Zhenyu
> > Division of Chemistry and Biological Chemistry
> > School of Physical and Mathematical Sciences
> > Nanyang Technological University
> > --
> > Gromacs Users mailing list
> >
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] non-bonded kernels for water

[Mark Abraham]

Hi,

This depends what cutoff scheme you are using. Only the group scheme has
interaction-specific kernels for water, and those are still available in
plain-C versions if you compile with GMX_SIMD=None. One would not really
call any of that "highly optimized." We don't encourage the use of any of
the above, but it's available for reference.

Mark

On Thu, Jul 23, 2015 at 6:30 PM Sikandar Mashayak 
wrote:

> Hi,
>
> I am wondering what non-bonded kernel is used for water simulations when
> gromacs is built with None SIMD option? Is it plainC or water specific
> highly optimized kernel? I understand that there are highly optimized
> kernels specific to water and are they still used even if SIMD=None?
>
> Thanks,
> Sikandar
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Re: [gmx-users] Linking contrib program issue

[Mark Abraham]

Hi,

Contrib is somewhere we put code that someone might find a use for, but we
do no work on it, so it's probably all broken.

For things like building your own analysis tool, check out the machinery in
share/template

Mark

On Thu, Jul 23, 2015 at 11:28 AM Michael Cristòfol Clough <
michaelcristo...@gmail.com> wrote:

> Hello everyone,
>
> A few months ago I wrote a program for gromos and I want to rewrite it for
> gromacs now. I was able to link the external xdr library to a simple
> program but in order to acces information in the topology I would like to
> link my program with the rest of gromacs, here is where I'm in trouble, I
> can't compile and install my program with the rest of gromacs. What I
> expected when I read the README file in the contrib directory was that I
> simply had to add my program's name, e.g. FOO.c, in the CMakeLists.txt,
> leaving it like this:
>
> set(CONTRIB_PROGRAMS
>  FOO
> )
>
> foreach(PROG ${CONTRIB_PROGRAMS})
> add_executable(${PROG} ${PROG}.c ${NGMX_COMMON_SOURCE})
> set_target_properties(${PROG} PROPERTIES OUTPUT_NAME
> "${PROG}${GMX_BINARY_SUFFIX}")
> endforeach(PROG)
>
> But it didn't work.
>
> One of the things I tried, to discart errors of my program, was to try to
> use existing programs in the contrib directory and add them to the
> CMakeLists.txt, but I couldn't compile them either.
>
> I supose there's a simple way to do this. I would really appreciate it if
> someone could give me a hand, telling me the usual procedure or with a link
> to some reference material I could look at. I hope I'm not asking for too
> much.
>
> Best regards,
>
> Michael
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Re: [gmx-users] Chlorine in PDBs

[Smith, Micholas D.]

Adam,

The topology file is the definitive atom-definiations used in the simulation. 
You just need to confirm that the Chlorine in your *.top has an matches the 
atomtype from  Amber99SB. As far as being written as C instead CL in the pdb, 
you could likely just use sed to find and replace these into CL so VMD treats 
them properly (a similar problem happens if you use OPLS and have calcium ions 
(name CA) vmd thinks they are all alpha-carbons).

-Micholas 

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of az 

Sent: Friday, July 24, 2015 4:26 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Chlorine in PDBs

Hi

Could someone enlighten me what are the "correct" (Gromacs-wise) atom
type and PDB column numbers for a chlorine substituent in a ligand ? I
use a MOE-written PDBs as MD input (Amber99SB), and if a chlorine is
present, its written as CL (both letters uppercase) in the 13th and 14th
column. Now when feeding that to acpype, the output PDB has a CL again,
but shifted to columns 14 and 15 and with a C in the last element
column. Seeing how this is similar to how box ions are written, I gave
it no heed, but now PDBs saved from a completed trajectory, display the
CL as a carbon in VMD, Chimera, or MOE. I can obviously edit that but
I'd like to be sure if my CLs are being treated as chlorines during the MD.

Input line:HETATM 2166 CL   PXN 0  -7.547  -4.598 6.977
1.00  0.00  CL
Post-acpype:ATOM 26  CL  PXN Z   1  -7.547  -4.598 6.977
1.00  0.00   C
Post-MD:ATOM   2147  CL  PXN B 169   2.196   0.709 5.879
1.002409.13

Cheers,
Adam
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Re: [gmx-users] Chlorine in PDBs

[az]

That's what I needed to hear! According to the topology the atom is 
perfectly fine.


Thanks a lot,
Adam

On 24-Jul-15 14:09, Smith, Micholas D. wrote:

Adam,

The topology file is the definitive atom-definiations used in the simulation. 
You just need to confirm that the Chlorine in your *.top has an matches the 
atomtype from  Amber99SB. As far as being written as C instead CL in the pdb, 
you could likely just use sed to find and replace these into CL so VMD treats 
them properly (a similar problem happens if you use OPLS and have calcium ions 
(name CA) vmd thinks they are all alpha-carbons).

-Micholas

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of az 

Sent: Friday, July 24, 2015 4:26 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Chlorine in PDBs

Hi

Could someone enlighten me what are the "correct" (Gromacs-wise) atom
type and PDB column numbers for a chlorine substituent in a ligand ? I
use a MOE-written PDBs as MD input (Amber99SB), and if a chlorine is
present, its written as CL (both letters uppercase) in the 13th and 14th
column. Now when feeding that to acpype, the output PDB has a CL again,
but shifted to columns 14 and 15 and with a C in the last element
column. Seeing how this is similar to how box ions are written, I gave
it no heed, but now PDBs saved from a completed trajectory, display the
CL as a carbon in VMD, Chimera, or MOE. I can obviously edit that but
I'd like to be sure if my CLs are being treated as chlorines during the MD.

Input line:HETATM 2166 CL   PXN 0  -7.547  -4.598 6.977
1.00  0.00  CL
Post-acpype:ATOM 26  CL  PXN Z   1  -7.547  -4.598 6.977
1.00  0.00   C
Post-MD:ATOM   2147  CL  PXN B 169   2.196   0.709 5.879
1.002409.13

Cheers,
Adam
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Re: [gmx-users] Linking contrib program issue

[Michael Cristòfol Clough]

Hi Mark,

Thank you for your reply. I modified template and it worked ok, but I
wanted to do it properly so that I can add more analysis tools. I'm quite a
newbie with Cmake and where I'm having trouble is adding more programes to
the CMake files. I'll look into it more, thank you.

Regards,

Michael

On 24 July 2015 at 13:41, Mark Abraham  wrote:

> Hi,
>
> Contrib is somewhere we put code that someone might find a use for, but we
> do no work on it, so it's probably all broken.
>
> For things like building your own analysis tool, check out the machinery in
> share/template
>
> Mark
>
> On Thu, Jul 23, 2015 at 11:28 AM Michael Cristòfol Clough <
> michaelcristo...@gmail.com> wrote:
>
> > Hello everyone,
> >
> > A few months ago I wrote a program for gromos and I want to rewrite it
> for
> > gromacs now. I was able to link the external xdr library to a simple
> > program but in order to acces information in the topology I would like to
> > link my program with the rest of gromacs, here is where I'm in trouble, I
> > can't compile and install my program with the rest of gromacs. What I
> > expected when I read the README file in the contrib directory was that I
> > simply had to add my program's name, e.g. FOO.c, in the CMakeLists.txt,
> > leaving it like this:
> >
> > set(CONTRIB_PROGRAMS
> >  FOO
> > )
> >
> > foreach(PROG ${CONTRIB_PROGRAMS})
> > add_executable(${PROG} ${PROG}.c ${NGMX_COMMON_SOURCE})
> > set_target_properties(${PROG} PROPERTIES OUTPUT_NAME
> > "${PROG}${GMX_BINARY_SUFFIX}")
> > endforeach(PROG)
> >
> > But it didn't work.
> >
> > One of the things I tried, to discart errors of my program, was to try to
> > use existing programs in the contrib directory and add them to the
> > CMakeLists.txt, but I couldn't compile them either.
> >
> > I supose there's a simple way to do this. I would really appreciate it if
> > someone could give me a hand, telling me the usual procedure or with a
> link
> > to some reference material I could look at. I hope I'm not asking for too
> > much.
> >
> > Best regards,
> >
> > Michael
> > --
> > Gromacs Users mailing list
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[gmx-users] Regarding engineered residue topology

[Venkat Reddy]

Dear all,
I am trying to simulate a peptide with engineered residues like Aib (alpha
amino-isobutyric acid). I am trying to use OPLS-aa forcefield. Though
everything went well initially during topology generation, grompp showed
the following error.

ERROR 1 [file topol.top, line 2316]:
  No default Ryckaert-Bell. types
ERROR 2 [file topol.top, line 2317]:
  No default Ryckaert-Bell. types
ERROR 3 [file topol.top, line 2318]:
  No default Ryckaert-Bell. types
ERROR 4 [file topol.top, line 2325]:
  No default Ryckaert-Bell. types
ERROR 5 [file topol.top, line 2326]:
  No default Ryckaert-Bell. types
ERROR 6 [file topol.top, line 2327]:
  No default Ryckaert-Bell. types

The cross-check with topolo.top identified the dihedral CB2-CA-CB1-HB11 is
throwing the error. My question is, even though the parameters for Aib are
available in OPLS ff, why I am getting this error?

Please help me in this regard

With regards
Venkat
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Re: [gmx-users] magnetic field - segmentation fault

[Maryam Kowsar]

Dear Erik,

Thank you! My sleeves are rolled up for several days! Which debugger do you
suggest?

Dear Man Hong,

It seems we are looking at the problem from 2 different angles. Well, I am
going to test it, but I think it's not logical; without T-coupling we can't
rely on the results. However, I wonder why you think it may cause problems.
Velocities should change. I guess I can ask you questions then. Which
version of gromacs are you working with? Which source codes have you
modified?
Thank you!

On Fri, Jul 24, 2015 at 8:41 AM, Man Hoang Viet  wrote:

> Hi Maryam Kowsar,
>
> I have implemented external magnetic field to GROMACS and tested it. The
> code ran well and the test result is consistent with experiment for simple
> case (say Na+ in vacuum and without t_coupling). I may guest why your code
> got the error. But I am sorry that I can not share my code to anyone now
> (but I will do share it to this forum in near future).
> However, there is an important issue that MD simulation with t_coupling
> always does re-scale velocity of all atoms to keep the given temperature
> and it strongly effect on the Lorentz Force of the external magnetic
> field. Otherwise, If the t_coupling is not applied, the system temperature
> will increase forever. Therefore, I wonder whether we really can estimate
> effect of the magnetic field on protein (or other target) in simulation?
>
>
> >On 23 Jul 2015, at 11:52, Maryam Kowsar  wrote:
>
> > Dear users,
> >
> > Iam trying to add magnetic field code to gromacs. I think I did all the
> > modifications necessary in all source codes but when I use mdrun command
> > it
> > gives me "segmentation fault" error while in md.log the magnetic field is
> > present. When I change tpx_version the error is gone but in md.log no
> > magnetic field is implemented. How can I overcome segmentation fault
> > error?  Should tpx_version be changed after adding a code?
> >
> > Thanks!
>
> Man Hoang Viet
> Institute of Physics,
> Polish Academy of Sciences.
> Al. Lotnikow 32/46
> 02-668 Warsaw, Poland.
>
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[gmx-users] regarding parallel tempering replica exchange

[Kumar Meena, Santosh]

Dear all,


I would like to do parallel tempering replica exchange with 6 replicas, but I 
am not getting the different variables to be used in md.mdp files (in all the 6 
mdp files ). I suppose, I have to make free-energy = yes and 
simulated-tempering =yes but then what values should I use for other parameters 
 for example for init-lambda ,  init-lambda-state and temperature-lambdas (see 
below). Could you please provide the mdp files for parallel tempering replica 
exchange for temperature ranging 300-550 K.

; Free energy variables
free-energy  = yes
couple-moltype   = 
couple-lambda0   = vdw-q
couple-lambda1   = vdw-q
couple-intramol  = no
init-lambda  = -1
init-lambda-state= -1
delta-lambda = 0
nstdhdl  = 50
fep-lambdas  = 
mass-lambdas = 
coul-lambdas = 
vdw-lambdas  = 
bonded-lambdas   = 
restraint-lambdas= 
temperature-lambdas  = 
calc-lambda-neighbors= 1
init-lambda-weights  = 
dhdl-print-energy= no
sc-alpha = 0
sc-power = 1
sc-r-power   = 6
sc-sigma = 0.3
sc-coul  = no
separate-dhdl-file   = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing  = 0.1



; simulated tempering variables
simulated-tempering  = yes
simulated-tempering-scaling = geometric
sim-temp-low = 300
sim-temp-high= 550
sim-temp-high= 300

Regards,
Santosh
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Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti)

[Eudes Fileti]

Hello Chris, I write to report the results of the tests you suggested.
To recap, I have two problems to solve. 1) The bad sampling around z = 0
and 2) the bumps along to the profile.

I solved the first discarding all the my initial configurations and
performing a new pulling (SMD). Only this time I used a higher force
constant (5000 kJ/mol nm2). Thus I got configurations close to z = 0, where
they were not generated.

For the second problem, you suggested recalculate the PMF using double
precision. The results of this test showed that it does not solve the
problem, on the contrary the bumps were even more pronounced, as indicated
by the plot in this link. https://goo.gl/photos/wGNhdyNG9pdqGfcB6

All tests were performed with prototypes simulations, with 40 windows of 2
ns spaced by 0.1 nm. A larger sample is obviously necessary for reliable
profiles, but this was enough to show the trend that I wanted to watch.

As I have mentioned before, I've done several tests aiming to eliminate
these bumps: use of higher sampling, up to 20ns per window; reducing the
spacing between the windows (from 0.1 to 0.05 nm); changing the spring
constant from 1000 up to 5000 kJ/mol nm2, use of two different versions of
the Gromacs (4.6 e 5.0) and also I tested it with two different sets of
initial settings.

None of this attempts solved the bumps problem.

If you (or someone else) have any other tips please let me know.

Thank you
eef

___
Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Rua Talim, 330, São José dos Campos - SP
Página: sites.google.com/site/fileti/

>
> --
>
> Message: 4
> Date: Wed, 22 Jul 2015 14:56:50 +
> From: Christopher Neale 
> To: "gmx-us...@gromacs.org" 
> Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0
> Message-ID:
> <
> blupr03mb18470a33a4e3ff149c95963c5...@blupr03mb184.namprd03.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Eudes:
>
> There are two issues: The first issue is the fact that you've got a
> sampling problem near the bilayer center. The second issue is the periodic
> bumps that you see in your PMFs. I'll take the second part first.
>
> The source of the periodic bumps in PMFs from umbrella sampling is, to me,
> a million dollar question. I've seen them in my own work. I've seen then in
> the literature (as you noted for Fig. 4 in
> http://www.mdpi.com/1422-0067/13/11/14451/htm ). I've seen them when
> people use g_wham and Alan Grossfield's version of WHAM. What I don't yet
> know is if people also see this when running US simulations with AMBER,
> CHARMM, or NAMD. Frankly, either answer scares me a little. If you see wild
> oscillations of the PMF, at large distances then one possible source is
> that you are near a distance that is half your box length along the order
> parameter. Note that with constant pressure simulations you will get
> oscillations in the length of the box and also when your membrane changes
> shape it could flip the vector of closest approach by 180 deg if you are
> close to the half-box limit. However, that should not be relevant to the
> bumps (out of interest, how large is your box along z?). Although I do
>  n't know what is going on with these PMF bumps, I also note that
> membranes as a whole always tend to migrate toward positive z and lipids
> tend to flow to positive x in gromacs simulations, so I wonder if it is a
> rounding issue. Could you try again with double precision and see if you
> get the bumps?
>
> As for the problem with sampling near the bilayer center... my first guess
> is that you've got some of your replicas on the wrong side of the bilayer's
> center. Did you intend to go across the center and sample also in the lower
> leaflet? I've only ever used gromacs 3 and 4 to do pulling simulations,
> never gmx 5. You can see my concerns about gmx5 for this type of issue near
> the bilayer center here:
> https://www.mail-archive.com/gromacs.org_gmx-users%40maillist.sys.kth.se/msg11324.html
> One simply has to test it. However, if gmx5 does indeed work properly with
> this new US philosophy, then I presume that you simply need to move your
> starting coordinates such that your solute is in the positive leaflet for
> all replicas. You can test this by visualization or g_dist, which reports
> the sign of the displacement (look in the 5th column I think for the z
> value). Note that you are using pull_start=yes, so which side of the
> bilayer your solute is initially on should make a difference here.
>
> Chris.
>
> -- original message:
>
> Hi Chris, a few days ago I posted a question on GMX list but unfortunately
> I not received an answer yet. So I write to you for help at your
> convenience.
> http://permalink.gmane.org/gmane.science.biology.gromacs.user/78439
>
> Besides the problem exposed the link above I'm trying to understand the
> importance of the relative distance between the COM. Due to fluctu

[gmx-users] gromos43a1p issue with ATP

[Saman Shahriyari]

Dear users


I am trying to run pdb2gmx on a protein holding ATP (with gromacs 467 and 
gromos43a1p.ff). However I have problem introducing ATP atom names in the input 
pdb file, based on the .rtp file of gromos43a1p (for example AO1PA is the name 
for an oxygen atom of ATP based on gromos43a1p .rtp. however pdb does not seem 
to know more than four characters for the atoms name and hence this pdb2gmx 
error prompts: atom AO1P was not found in .rtp ). Can anyone gives me a 
clue on this?Regards,Saman


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