[gmx-users] Apply position restraints to part of RNA molecule

[闫舒婷]

Dear gmx users,

I am working on simulating a RNA aptamer with GROMACS. I want to apply
position restraints to only part of the molecule during equilibration. I
created an .itp file including those atoms which I plan to make restrained.
I defined position restraints in .mdp file, and in the .top file, I also
included that ,itp file. I am not sure whether what I did is correct, for I
didn't observe a difference. I also tried to use -r flag with an ,gro file
including those atoms, when I used grompp. But there appeared fatal error
notification saying that the the number of atoms didn't match. I was also
thinking about doing something with the .top file for example writing three
molecule type instead of one, but I thought that might be crazy. I am
confused. Could anyone give me a hint? Thank you for your time.

Sincerely,
Shuting Yan
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Re: [gmx-users] Force Field for amino acid and peptide

[Justin Lemkul]

On 5/25/16 11:05 AM, Alexander Alexander wrote:

Dear Gromacs user,

I am going to simulate the binding free energy of some amino acid to a
metal surface in aqueous solution and also peptide adsorption behavior into
this surface.

I know the force field of the surface as well as the better type of water
for such a work, but I do not know which type of Force Filed could be the
better choice for the peptide (amino acids) for this simulation, so I would
be so appreciated if anybody could address me to a better choice of peptide
(amino acid) Force Filed for such a goal?



One that is compatible with the force field of the surface.  A force field is a 
self-consistent entity.  In general, you can't mix and match different parameter 
sets from different sources, unless those parameter sets have a common origin or 
shared method of parametrization.  So your choice here for treatment of the 
protein really isn't a free one, it's not about being the "better choice" for 
the system; there can be only one answer, if it exists.  Maybe there is no 
protein force field compatible with whatever the surface is.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] Generating topology for a HEM protein with CHARMM27

[Justin Lemkul]

On 5/25/16 9:58 AM, zeineb SI CHAIB wrote:

@Justin,

Thank you very much for your help, I finally fixed the problem but I'm having 
another one with grompp (which was expected): The error that I get is:

ERROR 7 [file topol.top, line 41571]:
  No default Proper Dih. types

Fatal error:
There were 13 errors in input file(s)

I think that the problem is about the bond parameters between SH in cystein and 
HEME iron group, isn't it?

After looking in the literature, I found their corresponding parameters: I 
added the following fields in CHARMM file ffbonded.it:








[
bondtypes ]
;
i   j  func b0   kb
  SG
  FE1  0.232  209200.0




[
angletypes ]
;
i   j   k   functh0 cth ub0 cub
CT2
   SG   FE   5  100.6   418.4   0.0 0.0
SG
FE   NPH  5   90.0   836.8   0.0 0.0
SG
FE   NPH  5   90.0   836.8   0.0 0.0
SG
FE   NPH  5   90.0   836.8   0.0 0.0
SG
FE   NPH  5   90.0   836.8   0.0 0.0

;
###
X   
 CS SS  X 9 0.200.0 3

CA
 CB  SG  FE  9   0.200.0   3
HB1
CB  SG  FE  9   0.200.0   3
HB1
CB  SG  FE  9   0.200.0   3

;
###
X   
 FE SS  X 9 0.000.0   4
CB
 SG  FE  NPH 9   0.000.0 4
CB
 SG  FE  NPH 9   0.000.0 4
CB
 SG  FE  NPH 9   0.000.0 4







But after that, I had another type of error:

Fatal error:
Unknown bond_atomtype SG






I added an SG entry in atomtypes.atp but I'm having the same error? Am I 
missing something?



SG is an atom *name*, not an atom *type*.

atomtypes.atp is also irrelevant anyway, as it is only read by pdb2gmx, so 
that's not how you add new atom types.  But in any case, this is not what you 
should be doing anyway.  Be careful that your protonation states are correct - 
make sure that -SH is correct (instead of the thiolate form) before adding a 
bunch of parameters and trying to do the simulation.


-Justin


Thank you very much for all your help and guidance Justin!

Regards.

Zeineb.



From: zeineb...@hotmail.com
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Generating topology for a HEM protein with CHARMM27
Date: Mon, 23 May 2016 10:31:05 +0100




I'm looking to generate the topology of a HEM protein , I choose CHARMM as a 
force field. At the begining, when I run pdb2gmx I had this error about missing 
hydrogen's:

WARNING:
atom HA is missing in residue HEM 473 in the pdb file

You
might need to add atom HA to the hydrogen database of building block
HEME

in
the file aminoacids.hdb (see the manual)






WARNING:
atom HB is missing in residue HEM 473 in the pdb file

You
might need to add atom HB to the hydrogen database of building block
HEME

in
the file aminoacids.hdb (see the manual)









---
Program
pdb2gmx, VERSION 4.6.5
Source
code file: /build/buildd/gromacs-4.6.5/src/kernel/pdb2top.c, line:
1588



Fatal
error:
There
were 30 missing atoms in molecule Other2, if you want to use this
incomplete topology anyhow, use the option -missing
For
more information and tips for troubleshooting, please check the
GROMACS
website
at http://www.gromacs.org/Documentation/Errors
---
After a research, I found what was missing: I made a copy of aminoacids.hdb 
(Charmm27.ff folder) in my working directory and I edited this file:
I added the following Lines:











HEME 16

1
  1   HA
 CHA C1A C4D
1
  1   HB
 CHB C4A C1B
1
  1   HC
 CHC C1C C4B
1
  1   HD
 CHD C1D C4C
3
  4   HMA
CMA C3A C2A
2
  6   HAA
CAA C2A
CBA
2
  6   HBA
CBA CAA
CGA
3
  4   HMB
CMB C2B C1B
1
  1   HAB
CAB C3B CBB
2
  3   HBB
CBB CAB C3B
3
  4   HMC
CMC C2C C1C
1
  1   HAC
CAC CBC C3C
2
  3   HBC
CBC CAC C3C
3
  4   HMD
CMD C2D C1D
2
  6   HAD
CAD C2D CBD
2
  6   HBD
CBD CAD CGD



I fixed the problem of missing hydrogens but I'm having another type of error:

Special Atom Distance matrix:
  HEM360  HEM360
CAB2CAC3
  HEM360CAC3   0.796
  HEM360FE43   0.557   0.557

---
Program gmx pdb2gmx, VERSION 5.1.2
Source code file: 
/home/francois/Bureau/Zineb/gromacs-5.1.2/src/gromacs/gmxpreprocess/resall.c, 
line: 645

Fatal error:
Residue 'HEM' not found in residue topology database
For more information and tips 

Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

[Szilárd Páll]

On Wed, May 25, 2016 at 8:20 PM, Uliano Guerrini 
wrote:

>
> > Il giorno 25 mag 2016, alle ore 16:30, Szilárd Páll <
> pall.szil...@gmail.com> ha scritto:
> >
> > On Wed, May 25, 2016 at 12:58 PM, Uliano Guerrini <
> uliano.guerr...@unimi.it > wrote:
> > On OSX 11.5 I instelled cuda 7.5, compiled samples and when I run:
> >
> > ./deviceQuery Starting...
> >
> >  CUDA Device Query (Runtime API) version (CUDART static linking)
> >
> > Detected 1 CUDA Capable device(s)
> >
> > Device 0: "GeForce GTX 680"
> >   CUDA Driver Version / Runtime Version  7.5 / 7.5
> >   CUDA Capability Major/Minor version number:3.0
> >   Total amount of global memory: 4096 MBytes (4294508544
> bytes)
> >   ...
> >
> > and so on, so I presume my CUDA installation is correct driver is ok and
> card is supported. Then I compiled from source using openMP enabled clang
> from macport (the one from apple is useless and gcc isn’t supported anymore
> by NVIDIA on OSX) configuring with:
> >
> > cmake ../gromacs-5.1.2 -DCMAKE_C_COMPILER=clang
> -DCMAKE_CXX_COMPILER=clang++ -DGMX_GPU=on -DCMAKE_PREFIX_PATH=/opt/local
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
> >
> > All goes apparently well, apart from:
> >
> > -- Could not detect NVIDIA GPUs
> >
> > and:
> >
> > -- Could NOT find NVML (missing:  NVML_LIBRARY NVML_INCLUDE_DIR)
> >
> > which I presume I can ignore as on OSX platform NVIDIA doesn’t offer
> NVML and GPU detection is based on that library (I also read on the net of
> people safely ignoring these warnings).
> >
> > Nevertheless when I run gmx mdrun I get the following message:
> >
> > NOTE: Error occurred during GPU detection:
> >   CUDA driver version is insufficient for CUDA runtime version
> >   Can not use GPU acceleration, will fall back to CPU kernels.
> >
> > My limited abilities (just some printf here and there) led me to find
> that the call to cudaGetDeviceCount on line 602 of the file gpu_utils.cu <
> http://gpu_utils.cu/> within gromacs/gmxlib/gpu_utils of the untarred
> 5.1.2 gromacs version fails.
> >
> > Any suggestions?
> >
> > Your questions are not related to development, please post such
> questions to the users' list (CCd, please continue there).
>
> Sorry for that, I gave an (admittedly fast) glance to user’s list and I
> found there lots of chemistry question so I subscribed to the wrong list.
> I’ll continue on the right one.
>

Thanks!


>
> >
> > Secondly, this is intriguing, could it be that you are using a newer
> runtime form a different path with GROMACS than with the deviceQuery SDK
> sample?
>
> I (believe to) have only one (CUDA?) runtime as I installed it today.
>

In that case, I'm not sure what could be the issue. Perhaps a dynamic
library path is missing? You can check with the equivalent of ldd on OS X.
The GROMACS log header should contain runtime and driver versions, what
does your log file show?


>
> >
> > BTW, I do think this should work, but to the best of my knowledge Apple
> has no official hardware that ships with or can be upgraded to GTX 680,
> right?
>
> Wrong: this is a macpro compatible (EFI firmware) GTX680 (now
> discontinued, there have been quite a lot out there, still easily found on
> ebay or similar) on a macpro 5,1 official Apple hardware.
>
> Apple itself didn’sell any GTX board (but sold some Quadro). They were
> however quite common among Adobe Suite (and  other software) users.
>

Thanks for the correction, I was not aware of that!

--
Szilárd



>
> uliano
>
> >
> > Cheers,
> > --
> > Szilárd
>
>
> --
> Gromacs Users mailing list
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> * Please search the archive at
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Re: [gmx-users] gromacs energy minimization fatal error: Invalid bond type 1000 in constant-PH MD

[Justin Lemkul]

On 5/25/16 9:21 AM, Wang Tao wrote:

Hi,Dr Justin!

You have mentioned that i missed my itp file.Here is it
##

[ moleculetype ]
;molnamenrexcl
 OHIN  1

[ atoms ]
;id  at type  res nr  residue name at name cg nr charge mass
1opls_434 1OHIN   OH  1   -1.300  15.999
2opls_435 1OHIN   HO  20.300  1.008

[ bonds ]
;i j funct lengthforce.c
 1 2  1 0.09450  462750.4;
##
As you can see, that is how i defined the itp file of OH-.

Those parameters can be found in oplsaa.ff/ffbonded.itp and 
oplsaa.ff/ffnonbonded.itp files.They have been provided in gromacs version 
4.6.7.
Here are they:
##

HOOH  10.09450   462750.4   ; SUG(OL) wlj mod 0.96-> 0.945
##

 opls_434   OH   8  15.99940-1.300   A3.2e-01  1.04600e+00
 opls_435   HO   1   1.00800 0.300   A0.0e+00  0.0e+00
##
But i really don't understand why the bond in OH- is invalid.Or in another 
word,what can i do to finish an sucessful energy minimization with OH- in my 
system?



No idea; it works for me.  I built a system of one OH- in vacuo, applied your 
topology, and it worked fine.  Probably something in the .top is broken, and 
#include statement in the wrong place or something else.


-Justin


You also said that waht i am conduncting is not a true constant PH MD.Yes,you 
are right.I did have some misunderstanding about it. But in my system ,i 
intended to create an environment where there is plenty of OH-with fixed 
concentration of it.So fixed protonation  is ok in this work. But anyway, i am 
very interested in constant-PH MD,and want to do something about it.I would 
spend more time on it.

Now,would you please offer me some advice on solve my problem above?

Tao Wang

Thank You!


Message: 2
Date: Wed, 25 May 2016 07:04:59 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gromacs energy minimization fatal error:
Invalid bond type 1000 in constant-PH MD
Message-ID: 
Content-Type: text/plain; charset=windows-1252; format=flowed



On 5/25/16 6:06 AM, Wang Tao wrote:

Hi,every one!

I'm using opls aa in gromacs to conduct constant-PH MD. In my system,PH is 
equal to 13.There are three kind of groups, NA+,OH- and H2O. The itp file for 
OH- is created by myself.



This is not what constant pH MD is.  You've got a fixed protonation state with
OH- floating around, which may not be physically realistic.


After having finished the genbox and genion steps sucessfully, i met a problem 
in energy minimization step. The output information says:Invalid bond type 
1000. But i don't really understand what the exact problem is.


Tried to remove bond definition in itp file for OH-, don't work.

Tried to remove bond definition in ffbonded.itp for OH-, don't work.

Replaced OH- with CL-,error infomation disappeared.


I believe the problem is related to OH- force field parameters,but don't know 
how to deal with it.



You haven't provided us with its topology, so there's nothing anyone can do but
guess haphazardly.  But if removing it solves the problem, you know exactly
where the issue is.

-Justin



Can anyone help me?


Tao Wang

Thank You!



--
==

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

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

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

==





--
==

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

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

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

==
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Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

[Uliano Guerrini]

> Il giorno 25 mag 2016, alle ore 16:30, Szilárd Páll  
> ha scritto:
> 
> On Wed, May 25, 2016 at 12:58 PM, Uliano Guerrini  > wrote:
> On OSX 11.5 I instelled cuda 7.5, compiled samples and when I run:
> 
> ./deviceQuery Starting...
> 
>  CUDA Device Query (Runtime API) version (CUDART static linking)
> 
> Detected 1 CUDA Capable device(s)
> 
> Device 0: "GeForce GTX 680"
>   CUDA Driver Version / Runtime Version  7.5 / 7.5
>   CUDA Capability Major/Minor version number:3.0
>   Total amount of global memory: 4096 MBytes (4294508544 
> bytes)
>   ...
> 
> and so on, so I presume my CUDA installation is correct driver is ok and card 
> is supported. Then I compiled from source using openMP enabled clang from 
> macport (the one from apple is useless and gcc isn’t supported anymore by 
> NVIDIA on OSX) configuring with:
> 
> cmake ../gromacs-5.1.2 -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ 
> -DGMX_GPU=on -DCMAKE_PREFIX_PATH=/opt/local  
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
> 
> All goes apparently well, apart from:
> 
> -- Could not detect NVIDIA GPUs
> 
> and:
> 
> -- Could NOT find NVML (missing:  NVML_LIBRARY NVML_INCLUDE_DIR)
> 
> which I presume I can ignore as on OSX platform NVIDIA doesn’t offer NVML and 
> GPU detection is based on that library (I also read on the net of people 
> safely ignoring these warnings).
> 
> Nevertheless when I run gmx mdrun I get the following message:
> 
> NOTE: Error occurred during GPU detection:
>   CUDA driver version is insufficient for CUDA runtime version
>   Can not use GPU acceleration, will fall back to CPU kernels.
> 
> My limited abilities (just some printf here and there) led me to find that 
> the call to cudaGetDeviceCount on line 602 of the file gpu_utils.cu 
>  within gromacs/gmxlib/gpu_utils of the untarred 5.1.2 
> gromacs version fails.
> 
> Any suggestions?
> 
> Your questions are not related to development, please post such questions to 
> the users' list (CCd, please continue there).

Sorry for that, I gave an (admittedly fast) glance to user’s list and I found 
there lots of chemistry question so I subscribed to the wrong list. I’ll 
continue on the right one.

> 
> Secondly, this is intriguing, could it be that you are using a newer runtime 
> form a different path with GROMACS than with the deviceQuery SDK sample?

I (believe to) have only one (CUDA?) runtime as I installed it today.

> 
> BTW, I do think this should work, but to the best of my knowledge Apple has 
> no official hardware that ships with or can be upgraded to GTX 680, right?

Wrong: this is a macpro compatible (EFI firmware) GTX680 (now discontinued, 
there have been quite a lot out there, still easily found on ebay or similar) 
on a macpro 5,1 official Apple hardware.

Apple itself didn’sell any GTX board (but sold some Quadro). They were however 
quite common among Adobe Suite (and  other software) users.

uliano

> 
> Cheers,
> --
> Szilárd


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[gmx-users] Force Field for amino acid and peptide

[Alexander Alexander]

Dear Gromacs user,

I am going to simulate the binding free energy of some amino acid to a
metal surface in aqueous solution and also peptide adsorption behavior into
this surface.

I know the force field of the surface as well as the better type of water
for such a work, but I do not know which type of Force Filed could be the
better choice for the peptide (amino acids) for this simulation, so I would
be so appreciated if anybody could address me to a better choice of peptide
(amino acid) Force Filed for such a goal?

Best regards,
Alex
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Re: [gmx-users] Surface tension coupling with Parrinello-Rahman algorithm

[Giuseppe Léonardo Licari]

Dear André,
In that publication it is specified the use of semi-isotropic pressure
coupling, not the surface-tension option in Gromacs. They were controlling
the surface tension applying a different pressure in XY than in Z. But I
guess it still different from my question, which is related to the
surface-tension option instead.

Regards,
Giuseppe

On 25/05/16 16:44, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of André Farias de Moura"
 wrote:

>I'd guess it works since it has been done already:
>http://www.sciencedirect.com/science/article/pii/S0005273613004501
>
>On Wed, May 25, 2016 at 10:31 AM, Giuseppe Léonardo Licari <
>giuseppe.lic...@unige.ch> wrote:
>
>> Dear all,
>> I have a question concerning the Surface-Tension pressure coupling in
>>NPT
>> simulation of a water/dodecane interface. In the Gromacs 5.1 manual it
>>is
>> reported that the coupling of the surface tension to the XY-plane works
>> only with Berendsen algorithm. I tried to do the MD simulation with
>> surface-tension coupling and Parrinello-Rahman algorithm and grompp did
>>not
>> complain. Also the simulation runs nicely and gives reasonable results.
>>So,
>> why is the simulation working with Surface-tension Parrinello-Rahman
>> coupling? Can I trust the result from this simulation?
>>
>> I thank you for the help and wish a really nice day.
>> Best regards,
>> Giuseppe
>>
>> p.s.: there was a previous discussion on this topic but without a real
>> answer to my points.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>
>-- 
>_
>
>Prof. Dr. André Farias de Moura
>Department of Chemistry
>Federal University of São Carlos
>São Carlos - Brazil
>phone: +55-16-3351-8090
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Re: [gmx-users] Surface tension coupling with Parrinello-Rahman algorithm

[André Farias de Moura]

I'd guess it works since it has been done already:
http://www.sciencedirect.com/science/article/pii/S0005273613004501

On Wed, May 25, 2016 at 10:31 AM, Giuseppe Léonardo Licari <
giuseppe.lic...@unige.ch> wrote:

> Dear all,
> I have a question concerning the Surface-Tension pressure coupling in NPT
> simulation of a water/dodecane interface. In the Gromacs 5.1 manual it is
> reported that the coupling of the surface tension to the XY-plane works
> only with Berendsen algorithm. I tried to do the MD simulation with
> surface-tension coupling and Parrinello-Rahman algorithm and grompp did not
> complain. Also the simulation runs nicely and gives reasonable results. So,
> why is the simulation working with Surface-tension Parrinello-Rahman
> coupling? Can I trust the result from this simulation?
>
> I thank you for the help and wish a really nice day.
> Best regards,
> Giuseppe
>
> p.s.: there was a previous discussion on this topic but without a real
> answer to my points.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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-- 
_

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Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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Re: [gmx-users] [gmx-developers] GTX 680 non detected on OS X

[Szilárd Páll]

On Wed, May 25, 2016 at 12:58 PM, Uliano Guerrini 
wrote:

> On OSX 11.5 I instelled cuda 7.5, compiled samples and when I run:
>
> ./deviceQuery Starting...
>
>  CUDA Device Query (Runtime API) version (CUDART static linking)
>
> Detected 1 CUDA Capable device(s)
>
> Device 0: "GeForce GTX 680"
>   CUDA Driver Version / Runtime Version  7.5 / 7.5
>   CUDA Capability Major/Minor version number:3.0
>   Total amount of global memory: 4096 MBytes (4294508544
> bytes)
>   ...
>
> and so on, so I presume my CUDA installation is correct driver is ok and
> card is supported. Then I compiled from source using openMP enabled clang
> from macport (the one from apple is useless and gcc isn’t supported anymore
> by NVIDIA on OSX) configuring with:
>
> cmake ../gromacs-5.1.2 -DCMAKE_C_COMPILER=clang
> -DCMAKE_CXX_COMPILER=clang++ -DGMX_GPU=on -DCMAKE_PREFIX_PATH=/opt/local
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
>
> All goes apparently well, apart from:
>
> -- Could not detect NVIDIA GPUs
>
> and:
>
> -- Could NOT find NVML (missing:  NVML_LIBRARY NVML_INCLUDE_DIR)
>
> which I presume I can ignore as on OSX platform NVIDIA doesn’t offer NVML
> and GPU detection is based on that library (I also read on the net of
> people safely ignoring these warnings).
>
> Nevertheless when I run gmx mdrun I get the following message:
>
> NOTE: Error occurred during GPU detection:
>   CUDA driver version is insufficient for CUDA runtime version
>   Can not use GPU acceleration, will fall back to CPU kernels.
>
> My limited abilities (just some printf here and there) led me to find that
> the call to cudaGetDeviceCount on line 602 of the file gpu_utils.cu
> within gromacs/gmxlib/gpu_utils of the untarred 5.1.2 gromacs version fails.
>
> Any suggestions?
>

Your questions are not related to development, please post such questions
to the users' list (CCd, please continue there).

Secondly, this is intriguing, could it be that you are using a newer
runtime form a different path with GROMACS than with the deviceQuery SDK
sample?

BTW, I do think this should work, but to the best of my knowledge Apple has
no official hardware that ships with or can be upgraded to GTX 680, right?

Cheers,
--
Szilárd


>
> uliano
>
>
>
>
>
>
>
>
>
>
>
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Re: [gmx-users] restraints between two different molecules

[Mark Abraham]

Hi,

On Wed, May 25, 2016 at 4:11 PM Rebeca García Fandiño 
wrote:

> Dear Gromacs users,
> I am trying to apply some distance restraints between two different
> molecules in a Gromacs simulation. I have read different things in the
> Gromacs list, such as both molecules should be in the same [atomtype]
> section (which is not the case)


In old versions, it is necessary to have such restraints within the same
moleculetype (not atomype, of course). This was because the system is built
from x copies of each moleculetype.

and also something related to the use of "pull_ngroups = 2". But it is not
> clear to me, and I don´t know how could I do it, even if this is possible.
> So, the question is...would it be possible to apply restraints between
> diferent molecules during a simulation?
>

GROMACS 5.1 introduces an [intermolecular_interactions] that precisely
addresses this issue without needing changes to [moleculetypes] or the use
of the pull code. Please see the documentaioin for details. :-)

Mark

Any help would be appreciated.
> Best wishes,
>
> Dr. Rebeca Garcia
> Santiago de Compostela University
> Spain
>
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Re: [gmx-users] Generating topology for a HEM protein with CHARMM27

[zeineb SI CHAIB]

@Justin, 

Thank you very much for your help, I finally fixed the problem but I'm having 
another one with grompp (which was expected): The error that I get is: 

ERROR 7 [file topol.top, line 41571]:
  No default Proper Dih. types

Fatal error:
There were 13 errors in input file(s)

I think that the problem is about the bond parameters between SH in cystein and 
HEME iron group, isn't it? 

After looking in the literature, I found their corresponding parameters: I 
added the following fields in CHARMM file ffbonded.it:








[
bondtypes ]
;
i   j  func b0   kb
  SG
  FE1  0.232  209200.0




[
angletypes ]
;
i   j   k   functh0 cth ub0 cub
CT2
   SG   FE   5  100.6   418.4   0.0 0.0
SG
FE   NPH  5   90.0   836.8   0.0 0.0
SG
FE   NPH  5   90.0   836.8   0.0 0.0
SG
FE   NPH  5   90.0   836.8   0.0 0.0
SG
FE   NPH  5   90.0   836.8   0.0 0.0

;
###
X   
 CS SS  X 9 0.200.0 3

CA
 CB  SG  FE  9   0.200.0   3
HB1
CB  SG  FE  9   0.200.0   3
HB1
CB  SG  FE  9   0.200.0   3

;
###
X   
 FE SS  X 9 0.000.0   4
CB
 SG  FE  NPH 9   0.000.0 4
CB
 SG  FE  NPH 9   0.000.0 4
CB
 SG  FE  NPH 9   0.000.0 4







But after that, I had another type of error:

Fatal error:
Unknown bond_atomtype SG






I added an SG entry in atomtypes.atp but I'm having the same error? Am I 
missing something? 

Thank you very much for all your help and guidance Justin!

Regards. 

Zeineb.  



From: zeineb...@hotmail.com
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Generating topology for a HEM protein with CHARMM27
Date: Mon, 23 May 2016 10:31:05 +0100




I'm looking to generate the topology of a HEM protein , I choose CHARMM as a 
force field. At the begining, when I run pdb2gmx I had this error about missing 
hydrogen's:

WARNING:
atom HA is missing in residue HEM 473 in the pdb file

You
might need to add atom HA to the hydrogen database of building block
HEME

in
the file aminoacids.hdb (see the manual)






WARNING:
atom HB is missing in residue HEM 473 in the pdb file

You
might need to add atom HB to the hydrogen database of building block
HEME

in
the file aminoacids.hdb (see the manual)









---
Program
pdb2gmx, VERSION 4.6.5
Source
code file: /build/buildd/gromacs-4.6.5/src/kernel/pdb2top.c, line:
1588



Fatal
error:
There
were 30 missing atoms in molecule Other2, if you want to use this
incomplete topology anyhow, use the option -missing
For
more information and tips for troubleshooting, please check the
GROMACS
website
at http://www.gromacs.org/Documentation/Errors
---
After a research, I found what was missing: I made a copy of aminoacids.hdb 
(Charmm27.ff folder) in my working directory and I edited this file: 
I added the following Lines: 











HEME 16 

1
  1   HA
 CHA C1A C4D
1
  1   HB
 CHB C4A C1B
1
  1   HC
 CHC C1C C4B
1
  1   HD
 CHD C1D C4C
3
  4   HMA
CMA C3A C2A
2
  6   HAA
CAA C2A
CBA
2
  6   HBA
CBA CAA
CGA
3
  4   HMB
CMB C2B C1B
1
  1   HAB
CAB C3B CBB
2
  3   HBB
CBB CAB C3B
3
  4   HMC
CMC C2C C1C
1
  1   HAC
CAC CBC C3C
2
  3   HBC
CBC CAC C3C
3
  4   HMD
CMD C2D C1D
2
  6   HAD
CAD C2D CBD
2
  6   HBD
CBD CAD CGD



I fixed the problem of missing hydrogens but I'm having another type of error:

Special Atom Distance matrix:
  HEM360  HEM360
CAB2CAC3
  HEM360CAC3   0.796
  HEM360FE43   0.557   0.557

---
Program gmx pdb2gmx, VERSION 5.1.2
Source code file: 
/home/francois/Bureau/Zineb/gromacs-5.1.2/src/gromacs/gmxpreprocess/resall.c, 
line: 645

Fatal error:
Residue 'HEM' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I added an entry in residuetype.dat (HEM  Protein), after making a copy in 
my working directory but it didn't fix the problem. I verified each file and 
they seem OK, I can't find where is the problem!!! Any help please!!!

Kind regards. 

Zeineb.
 

[gmx-users] Surface tension coupling with Parrinello-Rahman algorithm

[Giuseppe Léonardo Licari]

Dear all,
I have a question concerning the Surface-Tension pressure coupling in NPT 
simulation of a water/dodecane interface. In the Gromacs 5.1 manual it is 
reported that the coupling of the surface tension to the XY-plane works only 
with Berendsen algorithm. I tried to do the MD simulation with surface-tension 
coupling and Parrinello-Rahman algorithm and grompp did not complain. Also the 
simulation runs nicely and gives reasonable results. So, why is the simulation 
working with Surface-tension Parrinello-Rahman coupling? Can I trust the result 
from this simulation?

I thank you for the help and wish a really nice day.
Best regards,
Giuseppe

p.s.: there was a previous discussion on this topic but without a real answer 
to my points.
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 93

[Wang Tao]

Hi,Dr Justin!

You have mentioned that i missed my itp file.Here is it
##

[ moleculetype ]
;molnamenrexcl
 OHIN  1

[ atoms ]
;id  at type  res nr  residue name at name cg nr charge mass
1opls_434 1OHIN   OH  1   -1.300  15.999
2opls_435 1OHIN   HO  20.300  1.008

[ bonds ]
;i j funct lengthforce.c
 1 2  1 0.09450  462750.4; 
##
As you can see, that is how i defined the itp file of OH-.

Those parameters can be found in oplsaa.ff/ffbonded.itp and 
oplsaa.ff/ffnonbonded.itp files.They have been provided in gromacs version 
4.6.7.
Here are they:
##

HOOH  10.09450   462750.4   ; SUG(OL) wlj mod 0.96-> 0.945
##

 opls_434   OH   8  15.99940-1.300   A3.2e-01  1.04600e+00
 opls_435   HO   1   1.00800 0.300   A0.0e+00  0.0e+00
##
But i really don't understand why the bond in OH- is invalid.Or in another 
word,what can i do to finish an sucessful energy minimization with OH- in my 
system?

You also said that waht i am conduncting is not a true constant PH MD.Yes,you 
are right.I did have some misunderstanding about it. But in my system ,i 
intended to create an environment where there is plenty of OH-with fixed 
concentration of it.So fixed protonation  is ok in this work. But anyway, i am 
very interested in constant-PH MD,and want to do something about it.I would 
spend more time on it.

Now,would you please offer me some advice on solve my problem above?

Tao Wang
 
Thank You! 


Message: 2
Date: Wed, 25 May 2016 07:04:59 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gromacs energy minimization fatal error:
Invalid bond type 1000 in constant-PH MD
Message-ID: 
Content-Type: text/plain; charset=windows-1252; format=flowed



On 5/25/16 6:06 AM, Wang Tao wrote:
> Hi,every one!
>
> I'm using opls aa in gromacs to conduct constant-PH MD. In my system,PH is 
> equal to 13.There are three kind of groups, NA+,OH- and H2O. The itp file for 
> OH- is created by myself.
>

This is not what constant pH MD is.  You've got a fixed protonation state with
OH- floating around, which may not be physically realistic.

> After having finished the genbox and genion steps sucessfully, i met a 
> problem in energy minimization step. The output information says:Invalid bond 
> type 1000. But i don't really understand what the exact problem is.
>
>
> Tried to remove bond definition in itp file for OH-, don't work.
>
> Tried to remove bond definition in ffbonded.itp for OH-, don't work.
>
> Replaced OH- with CL-,error infomation disappeared.
>
>
> I believe the problem is related to OH- force field parameters,but don't know 
> how to deal with it.
>

You haven't provided us with its topology, so there's nothing anyone can do but
guess haphazardly.  But if removing it solves the problem, you know exactly
where the issue is.

-Justin

>
> Can anyone help me?
>
>
> Tao Wang
>
> Thank You!
>

--
==

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

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

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

==



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Re: [gmx-users] a suitable forcefield for ions

[Justin Lemkul]

On 5/25/16 8:49 AM, Nilkanta Chowdhury wrote:

Hello team,

how can I simulate a protein bind with FE4S4 in gromacs.
How to generate the topology.


Please start a new thread if you have an unrelated question, rather than 
hijacking someone else's topic.


This question has come up before; I don't know if there are good force fields 
for such species due to the complexity of their nature.  Try Google.


-Justin


Thank you..

On Wed, May 25, 2016 at 5:12 PM, Justin Lemkul  wrote:




On 5/25/16 7:40 AM, mah maz wrote:


Thanks Justin. I can only find atoms in ffnonbonded.itp in Amber ff. Where
should I search for ions parameters in Amber ff?



Every force field has an ions.itp file.  Look for those atom types.  But
knowing those values won't really tell you anything on their own.  You need
to know (1) the literature source of those parameters and (2) the pros/cons
to those parameters, also in the literature.

-Justin

On Wed, May 25, 2016 at 4:01 PM, mah maz  wrote:


Thanks Erik. I found nonbonded parameters for atoms only in Amber ff. Can

I use them for ions or they are already for ions?
eg. for Na sigma= 0.332 and epsilon=0.0115. Does it mean that we can use
thIS sigma and epsilon for Na+?

On Wed, May 25, 2016 at 2:11 PM, mah maz  wrote:

Hi all,


i need forcefield parameters for ions. can anyone tell me which
forcefield contains ions? can i do ion simulations with amber ff?

Thank you






--
==

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

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

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

==
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--
==

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

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

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

==
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Re: [gmx-users] a suitable forcefield for ions

[Nilkanta Chowdhury]

Hello team,

how can I simulate a protein bind with FE4S4 in gromacs.
How to generate the topology.
Thank you..

On Wed, May 25, 2016 at 5:12 PM, Justin Lemkul  wrote:

>
>
> On 5/25/16 7:40 AM, mah maz wrote:
>
>> Thanks Justin. I can only find atoms in ffnonbonded.itp in Amber ff. Where
>> should I search for ions parameters in Amber ff?
>>
>>
> Every force field has an ions.itp file.  Look for those atom types.  But
> knowing those values won't really tell you anything on their own.  You need
> to know (1) the literature source of those parameters and (2) the pros/cons
> to those parameters, also in the literature.
>
> -Justin
>
> On Wed, May 25, 2016 at 4:01 PM, mah maz  wrote:
>>
>> Thanks Erik. I found nonbonded parameters for atoms only in Amber ff. Can
>>> I use them for ions or they are already for ions?
>>> eg. for Na sigma= 0.332 and epsilon=0.0115. Does it mean that we can use
>>> thIS sigma and epsilon for Na+?
>>>
>>> On Wed, May 25, 2016 at 2:11 PM, mah maz  wrote:
>>>
>>> Hi all,

 i need forcefield parameters for ions. can anyone tell me which
 forcefield contains ions? can i do ion simulations with amber ff?

 Thank you


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

[Justin Lemkul]

On 5/25/16 7:40 AM, mah maz wrote:

Thanks Justin. I can only find atoms in ffnonbonded.itp in Amber ff. Where
should I search for ions parameters in Amber ff?



Every force field has an ions.itp file.  Look for those atom types.  But knowing 
those values won't really tell you anything on their own.  You need to know (1) 
the literature source of those parameters and (2) the pros/cons to those 
parameters, also in the literature.


-Justin


On Wed, May 25, 2016 at 4:01 PM, mah maz  wrote:


Thanks Erik. I found nonbonded parameters for atoms only in Amber ff. Can
I use them for ions or they are already for ions?
eg. for Na sigma= 0.332 and epsilon=0.0115. Does it mean that we can use
thIS sigma and epsilon for Na+?

On Wed, May 25, 2016 at 2:11 PM, mah maz  wrote:


Hi all,

i need forcefield parameters for ions. can anyone tell me which
forcefield contains ions? can i do ion simulations with amber ff?

Thank you






--
==

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

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

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

==
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Re: [gmx-users] a suitable forcefield for ions

[mah maz]

Thanks Justin. I can only find atoms in ffnonbonded.itp in Amber ff. Where
should I search for ions parameters in Amber ff?

On Wed, May 25, 2016 at 4:01 PM, mah maz  wrote:

> Thanks Erik. I found nonbonded parameters for atoms only in Amber ff. Can
> I use them for ions or they are already for ions?
> eg. for Na sigma= 0.332 and epsilon=0.0115. Does it mean that we can use
> thIS sigma and epsilon for Na+?
>
> On Wed, May 25, 2016 at 2:11 PM, mah maz  wrote:
>
>> Hi all,
>>
>> i need forcefield parameters for ions. can anyone tell me which
>> forcefield contains ions? can i do ion simulations with amber ff?
>>
>> Thank you
>>
>
>
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Re: [gmx-users] a suitable forcefield for ions

[Justin Lemkul]

On 5/25/16 7:31 AM, mah maz wrote:

Thanks Erik. I found nonbonded parameters for atoms only in Amber ff. Can I
use them for ions or they are already for ions?
eg. for Na sigma= 0.332 and epsilon=0.0115. Does it mean that we can use
thIS sigma and epsilon for Na+?



You should spend some time in the literature; there is a long history of ion 
parametrization and refinement, with subsequent discussion of which parameters 
are best for what application.  This is not an issue that is solved simply by 
perusing GROMACS force field files.


All of the force fields in GROMACS have ion parameters; it's up to you to decide 
which, if any, of these is suitable for whatever type of simulation(s) you want 
to do.


-Justin


On Wed, May 25, 2016 at 2:11 PM, mah maz  wrote:


Hi all,

i need forcefield parameters for ions. can anyone tell me which forcefield
contains ions? can i do ion simulations with amber ff?

Thank you



--
==

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

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

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

==
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Re: [gmx-users] a suitable forcefield for ions

[mah maz]

Thanks Erik. I found nonbonded parameters for atoms only in Amber ff. Can I
use them for ions or they are already for ions?
eg. for Na sigma= 0.332 and epsilon=0.0115. Does it mean that we can use
thIS sigma and epsilon for Na+?

On Wed, May 25, 2016 at 2:11 PM, mah maz  wrote:

> Hi all,
>
> i need forcefield parameters for ions. can anyone tell me which forcefield
> contains ions? can i do ion simulations with amber ff?
>
> Thank you
>
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Re: [gmx-users] Simulating conjugated protein

[Justin Lemkul]

On 5/25/16 12:55 AM, Sanket Ghawali wrote:

Dear, gmx-users,

Hello everyone,

I'm simulating a peptide in an SDS micelle, where my peptide is conjugated
to a organic compound at the N terminal. The SDS micelle was genrated using
CHARMM-GUI, here I am stuck with a problem for adding atom types for the
compound. I tried adding atomtypes for the compound into the .rtp files of
the CHARMM forcefield but when i try to run pdb2gmx it throws an error
regarding missing residues in .hdb file.

I edited the .hdb file adding the hydrogen atom information for the unknown
compound. The pdb2gmx worked this time but it throws back an error while
adding ions.

I tried using SwissParam to parameterized the unknown molecule, using this
i find that the compound does not remain bound to the peptide at the N
terminal even after merging the compound and peptide co ordinates.

The errors which i get while adding ions:

ERROR 190 [file topol.top, line 3284]:
  No default Proper Dih. types


ERROR 191 [file topol.top, line 3285]:
  No default Proper Dih. types


ERROR 192 [file topol.top, line 3286]:
  No default Proper Dih. types

Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 3 bonded neighbours molecule type 'SDS'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'

NOTE 1 [file topol.top, line 3377]:
  System has non-zero total charge: 17.180007
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.




---
Program grompp, VERSION 4.6.5
Source code file: /root/Downloads/gromacs-4.6.5/src/kernel/grompp.c, line: 563

Fatal error:
number of coordinates in coordinate file (sol.gro, 15465)
 does not match topology (topol.top, 15450)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Being Great is Not So Good" (Red Hot Chili Peppers)

.


Any suggestions on how to go about doing this?



http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue

You need to properly parametrize the residue in question first, including the 
whole linkage.  Based on the missing parameters and the suspicious charge, your 
underlying parametrization is not functional.


-Justin

--
==

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

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
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Re: [gmx-users] Combining various Flat-bottomed Potentials

[Justin Lemkul]

On 5/25/16 1:44 AM, jagannath mondal wrote:

Hi
  I am also interested in the issue of using a  flat-bottomed restraint,
for a spherocylinder.
 However, I am not sure whether the current gromacs settings of even a
linear combination of a sphere and cylinder can help here to generate a
spherocylinder.

If we put the spherical and cylindrical restraint on the same particle
(under the [position restraints] flag as Justin and Chris has suggested ),
the particle will be either be in a spherical confinement or in a
cylindrical confinement .  But for a spherocylinder, we need two
hemispheres which are capped on the two ends of a cylinder.
Hence, for a spherocylindrical restraint, what is needed here is a
restraint which will restrain the particle on going out when the z
coordinate of the particle exceeds the diameter of the cylinder AND the
sqrt(x**2+y**2) of the particle exceeds the length of the cylinder.
I am wondering whether this is possible within the current gromacs
implentation.
If it is not, I was interested in editing the source code relevant for flat
bottomed potential, to implement it for a spherocylinder. Is the following
path within gromacs directory right place to make the changes ?
  gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c



Yes, it is.

You basically need to create a hemisphere mode.  The cylinder restraint does not 
act parallel to the cylinder axis, so the restraint at the ends just needs to be 
enforced by the hemisphere.


-Justin

--
==

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

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

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

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Re: [gmx-users] gromacs energy minimization fatal error: Invalid bond type 1000 in constant-PH MD

[Justin Lemkul]

On 5/25/16 6:06 AM, Wang Tao wrote:

Hi,every one!

I'm using opls aa in gromacs to conduct constant-PH MD. In my system,PH is 
equal to 13.There are three kind of groups, NA+,OH- and H2O. The itp file for 
OH- is created by myself.



This is not what constant pH MD is.  You've got a fixed protonation state with 
OH- floating around, which may not be physically realistic.



After having finished the genbox and genion steps sucessfully, i met a problem 
in energy minimization step. The output information says:Invalid bond type 
1000. But i don't really understand what the exact problem is.


Tried to remove bond definition in itp file for OH-, don't work.

Tried to remove bond definition in ffbonded.itp for OH-, don't work.

Replaced OH- with CL-,error infomation disappeared.


I believe the problem is related to OH- force field parameters,but don't know 
how to deal with it.



You haven't provided us with its topology, so there's nothing anyone can do but 
guess haphazardly.  But if removing it solves the problem, you know exactly 
where the issue is.


-Justin



Can anyone help me?


Tao Wang

Thank You!



--
==

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

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

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

==
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Re: [gmx-users] Unusual bond

[Justin Lemkul]

On 5/25/16 6:47 AM, Alexander Alexander wrote:

Dear Gromacs user,

The VMD report below warning when I load my minimized ".gro" structure;

Warning) Unusual bond between residues:  13724 (none) and 22887 (waters).

The VMD does not report any warning when I load my structure "gro" file
before energy minimization, but when I minimized it in orde via "steep and
cg" integrator, this shows up for the final structure while the force has
already met the criteria and potential also nicely shows a negative
convergence.

I was wondering if this warning has something to be worried about?



VMD guesses where bonds should be based on distance.  It often gets them wrong. 
The topology is definitive; VMD is not.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] a suitable forcefield for ions

[Erik Marklund]

Hi,

Which ions? The monovalent ions commonly used with Amber have a tendency to 
cluster in unrealistic ways at moderate concentrations if memory serves me 
right.

Kind regards,
Erik

> On 25 May 2016, at 10:41, mah maz  wrote:
> 
> Hi all,
> 
> i need forcefield parameters for ions. can anyone tell me which forcefield
> contains ions? can i do ion simulations with amber ff?
> 
> Thank you
> -- 
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[gmx-users] Unusual bond

[Alexander Alexander]

Dear Gromacs user,

The VMD report below warning when I load my minimized ".gro" structure;

Warning) Unusual bond between residues:  13724 (none) and 22887 (waters).

The VMD does not report any warning when I load my structure "gro" file
before energy minimization, but when I minimized it in orde via "steep and
cg" integrator, this shows up for the final structure while the force has
already met the criteria and potential also nicely shows a negative
convergence.

I was wondering if this warning has something to be worried about?

Thanks.

Cheers,
Alex
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Re: [gmx-users] Installing GROMACS 5.1.2 om GPU

[Mark Abraham]

Hi,

You need to follow Intel's instructions for accessing the compiler -
including running their magic scripts from each shell that you want to
compile from. (Or save yourself some pain, use gcc, and probably run
slightly faster.)

Mark

‪On Wed, May 25, 2016 at 10:43 AM ‫יוכבד‬‎  wrote:‬

> Hi
>
> I've been having lots of trouble installing gromacs on our GPU machine.
>
> I have Intel2015 Compilers on my machine which are identified correctly
> during configuration.
>
> /private/gnss/cmake-2.8.11.2/bin/cmake ..
> -DCMAKE_INSTALL_PREFIX=/private/gnss/gromacs-5.1.2
> -DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.5/
> -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_FFT_LIBRARY=mkl
> -DMKL_LIBRARIES=$MKLROOT/lib/intel64 -DMKL_INCLUDE_DIR=$MKLROOT/include
>
> However when I run the make I get alot of warnings and finally the
> following error:
>
> /private/gnss/gromacs-5.1.2/src/external/boost/boost/config/compiler/in
> tel.hpp(93): remark #193: zero used for undefined preprocessing identifier
> "_WCHAR_T_DEFINED"
> # if ((_WCHAR_T_DEFINED + 0) == 0) && ((_WCHAR_T + 0) == 0)
> ^
>
> Linking CXX executable ../../bin/template
> ld: warning: libimf.so, needed by ../../lib/libgromacs.so.1.2.0, not found
> (try using -rpath or -rpath-link)
> ld: warning: libsvml.so, needed by ../../lib/libgromacs.so.1.2.0, not found
> (try using -rpath or -rpath-link)
> ld: warning: libirng.so, needed by ../../lib/libgromacs.so.1.2.0, not found
> (try using -rpath or -rpath-link)
> ld: warning: libintlc.so.5, needed by ../../lib/libgromacs.so.1.2.0, not
> found (try using -rpath or -rpath-link)
> ld: ../../bin/template: hidden symbol `__intel_cpu_features_init_x' in
>
> /opt/intel/composer_xe_2015.5.223/compiler/lib/intel64/libirc.a(cpu_feature_disp.o)
> is referenced by DSO
> ld: final link failed: Nonrepresentable section on output
> make[2]: *** [bin/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error 2
>
> all the files which are not found do exist in the compiler libraries and it
> is added to my path.
>
> Any suggestions how to solve this?
>
> Thanks
>
> Yocheved
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[gmx-users] gromacs energy minimization fatal error: Invalid bond type 1000 in constant-PH MD

[Wang Tao]

Hi,every one!

I'm using opls aa in gromacs to conduct constant-PH MD. In my system,PH is 
equal to 13.There are three kind of groups, NA+,OH- and H2O. The itp file for 
OH- is created by myself.

After having finished the genbox and genion steps sucessfully, i met a problem 
in energy minimization step. The output information says:Invalid bond type 
1000. But i don't really understand what the exact problem is.


Tried to remove bond definition in itp file for OH-, don't work.

Tried to remove bond definition in ffbonded.itp for OH-, don't work.

Replaced OH- with CL-,error infomation disappeared.


I believe the problem is related to OH- force field parameters,but don't know 
how to deal with it.


Can anyone help me?


Tao Wang

Thank You!
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Re: [gmx-users] mdrun terminated with errors with gromacs 5.1 in parallel

[Mark Abraham]

Hi,

The command

/app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi

isn't what you used to start the simulation - it couldn't work. Please copy
and paste actual things, and do also check out the advice in the install
guide about how to get access to installed versions of GROMACS by source
GMXRC.

Investigate that checkpoint file, e.g. ls -l. If you ran the first
simulation as root and now with your normal user, then things will not be
allowed... (don't use root for anything except make install).

For the second part, make sure your MPI system is working, e.g. by running
some other MPI test program. If there's a GROMACS problem, then you'll have
to look elsewhere in the output files to understand where it starts.

Mark

On Wed, May 25, 2016 at 10:30 AM Antara mazumdar 
wrote:

> Dear Gromacs users,
>
>I was trying to do equilibration of a mixed lipid vesicle using gromacs
> 5.1 in parallel.
> My pbs script file details for this is the following :
>
> /home/lipi/openmpi164/bin/mpirun -np 48
> /app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi -deffnm
> step6.2_equilibration -rdd 1.8 > test.dat
>
>
> However, the mdrun is terminated with the following two errors.
>
> *1)Cannot rename checkpoint file; maybe you are out of disk space?*
>
> i have checked the disk space, it still has terabytes of space left to be
> used. The folder where i am running it is hardly 45 MB.
>
>
> *2)mpirun noticed that process rank 10 with PID 62690 on node cn0013 exited
> on signal 11 (Segmentation fault).*
> Can anyone suggest me how to resolve it?
>
>
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
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[gmx-users] a suitable forcefield for ions

[mah maz]

Hi all,

i need forcefield parameters for ions. can anyone tell me which forcefield
contains ions? can i do ion simulations with amber ff?

Thank you
-- 
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[gmx-users] Installing GROMACS 5.1.2 om GPU

[יוכבד]

Hi

I've been having lots of trouble installing gromacs on our GPU machine.

I have Intel2015 Compilers on my machine which are identified correctly
during configuration.

/private/gnss/cmake-2.8.11.2/bin/cmake ..
-DCMAKE_INSTALL_PREFIX=/private/gnss/gromacs-5.1.2
-DGMX_GPU=on -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.5/
-DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_FFT_LIBRARY=mkl
-DMKL_LIBRARIES=$MKLROOT/lib/intel64 -DMKL_INCLUDE_DIR=$MKLROOT/include

However when I run the make I get alot of warnings and finally the
following error:

/private/gnss/gromacs-5.1.2/src/external/boost/boost/config/compiler/in
tel.hpp(93): remark #193: zero used for undefined preprocessing identifier
"_WCHAR_T_DEFINED"
# if ((_WCHAR_T_DEFINED + 0) == 0) && ((_WCHAR_T + 0) == 0)
^

Linking CXX executable ../../bin/template
ld: warning: libimf.so, needed by ../../lib/libgromacs.so.1.2.0, not found
(try using -rpath or -rpath-link)
ld: warning: libsvml.so, needed by ../../lib/libgromacs.so.1.2.0, not found
(try using -rpath or -rpath-link)
ld: warning: libirng.so, needed by ../../lib/libgromacs.so.1.2.0, not found
(try using -rpath or -rpath-link)
ld: warning: libintlc.so.5, needed by ../../lib/libgromacs.so.1.2.0, not
found (try using -rpath or -rpath-link)
ld: ../../bin/template: hidden symbol `__intel_cpu_features_init_x' in
/opt/intel/composer_xe_2015.5.223/compiler/lib/intel64/libirc.a(cpu_feature_disp.o)
is referenced by DSO
ld: final link failed: Nonrepresentable section on output
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2

all the files which are not found do exist in the compiler libraries and it
is added to my path.

Any suggestions how to solve this?

Thanks

Yocheved
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[gmx-users] mdrun terminated with errors with gromacs 5.1 in parallel

[Antara mazumdar]

Dear Gromacs users,

   I was trying to do equilibration of a mixed lipid vesicle using gromacs
5.1 in parallel.
My pbs script file details for this is the following :

/home/lipi/openmpi164/bin/mpirun -np 48
/app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi -deffnm
step6.2_equilibration -rdd 1.8 > test.dat


However, the mdrun is terminated with the following two errors.

*1)Cannot rename checkpoint file; maybe you are out of disk space?*

i have checked the disk space, it still has terabytes of space left to be
used. The folder where i am running it is hardly 45 MB.


*2)mpirun noticed that process rank 10 with PID 62690 on node cn0013 exited
on signal 11 (Segmentation fault).*
Can anyone suggest me how to resolve it?


Kind Regards,
Antara

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Re: [gmx-users] QMMM grompp error atom numbers fields.

[Groenhof, Gerrit]

Hi,

this is weird. I assume you've put the *'s only in your email?

Could you send me (off list) the mdp, index, top and gro file? Perhaps 
something else, such as missing link atom triggers the error message 
incorrectly.

Gerrit


Subject: [gmx-users] QMMM grompp error atom numbers fields.
Message-ID:

Content-Type: text/plain; charset=UTF-8

Dear members,

I am trying to run a QMMM simulation  in Gromacs4.5.5 using amber99sb-ILDN
together with orca. When I tried to run grompp I obtain the following error:






*  It appears as if you are trying to run a QM/MM calculation, but the
force  field you are using does not contain atom numbers fields. This is
an  optional field (introduced in Gromacs 3.3) for general runs, but
mandatory  for QM/MM. The good news is that it is easy to add - put the
atom number as  an integer just before the mass column in ffXXXnb.itp.  NB:
United atoms have the same atom numbers as normal ones.*

When I go through the forcefield itp file at
share/top/amber99sb-ildn.ff/ffnonbonded.itp I have seen that this
forcefield has an atom number column, or at least I have understood that it
is

[ atomtypes ]
; name  *at.num*  mass charge ptype  sigma  epsilon
Br  *35*  79.900.  A   0.0e+00  0.0e+00
C   * 6 * 12.010.  A   3.39967e-01  3.59824e-01
CA   *6*  12.010.  A   3.39967e-01  3.59824e-01
CB   *6 * 12.010.  A   3.39967e-01  3.59824e-01
CC   *6 * 12.010.  A   3.39967e-01  3.59824e-01


The 'at. num' column is the atom number? If it is, how can I solve this
error? Could you help me with that?


Thanks in advance,

Melchor Sanchez-Martinez

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