Re: [gmx-users] Regarding creating indexing with atoms having same labelling in different molecules

[Tasneem Kausar]

Try this
1 | 13 & a N
This will select the group 1 and 13 and all the atom having atom ID N.

On Tue, Jul 11, 2017 at 12:19 PM, Dilip H N 
wrote:

> Hello,
> I am having problems during creating the indexes for atoms which have same
> atom labelling for the two/three different molecules in the system (say
> nitrogen atom that is labelled as N in both the molecules).
>  whn i gave the command:-
> gmx make_ndx -f md.gro -o a.ndx
> i am getting the prompt as :-
> Reading structure file
> Going to read 0 old index file(s)
> Analysing residue names:
> There are: 1Protein residues
> There are:10  Other residues
> There are:   200  Water residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
>
>   0 System   :  750 atoms
>   1 Protein:10 atoms
>   2 Protein-H: 5 atoms
>   3 C-alpha  : 1 atoms
>   4 Backbone   : 3 atoms
>   5 MainChain  : 3 atoms
>   6 MainChain+Cb   : 3 atoms
>   7 MainChain+H : 6 atoms
>   8 SideChain  : 4 atoms
>   9 SideChain-H  : 2 atoms
>  10 Prot-Masses :10 atoms
>  11 non-Protein   :  890 atoms
>  12 Other:   140 atoms
>  13 TMAO  :   140 atoms
>  14 Water   :   600 atoms
>  15 SOL :   600 atoms
>  16 non-Water   :   374 atoms
>
> Here i need say the nitrogen present in protein (1 protein: 10 atoms) index
> and the nitrogen's present in tmao (13 TMAO: 140 atoms) in the .ndx
> file.ie.,
> i need the nitrogen present in protein and nitrogen's present in tmao in
> the index file..
> How can i get this..?? wht will be the commands for this... i tried with
> various commands but in vain
>
>
> Thank you...
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>  Sent with Mailtrack
>  referral=cy16f01.di...@nitk.edu.in&idSignature=22>
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Re: [gmx-users] Regarding creating indexing with atoms having same labelling in different molecules

[Mark Abraham]

Hi,

That is, Tasneem's recipe will find all atoms that are in group 1 OR group
13, AND whose name is N. If Dilip just wants the atoms in group 1 AND whose
name is N, then e.g.

1 & a N

There are some examples in the interactive help of gmx make_ndx

Mark

On Tue, Jul 11, 2017 at 9:14 AM Tasneem Kausar 
wrote:

> Try this
> 1 | 13 & a N
> This will select the group 1 and 13 and all the atom having atom ID N.
>
> On Tue, Jul 11, 2017 at 12:19 PM, Dilip H N 
> wrote:
>
> > Hello,
> > I am having problems during creating the indexes for atoms which have
> same
> > atom labelling for the two/three different molecules in the system (say
> > nitrogen atom that is labelled as N in both the molecules).
> >  whn i gave the command:-
> > gmx make_ndx -f md.gro -o a.ndx
> > i am getting the prompt as :-
> > Reading structure file
> > Going to read 0 old index file(s)
> > Analysing residue names:
> > There are: 1Protein residues
> > There are:10  Other residues
> > There are:   200  Water residues
> > Analysing Protein...
> > Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> > into groups...
> >
> >   0 System   :  750 atoms
> >   1 Protein:10 atoms
> >   2 Protein-H: 5 atoms
> >   3 C-alpha  : 1 atoms
> >   4 Backbone   : 3 atoms
> >   5 MainChain  : 3 atoms
> >   6 MainChain+Cb   : 3 atoms
> >   7 MainChain+H : 6 atoms
> >   8 SideChain  : 4 atoms
> >   9 SideChain-H  : 2 atoms
> >  10 Prot-Masses :10 atoms
> >  11 non-Protein   :  890 atoms
> >  12 Other:   140 atoms
> >  13 TMAO  :   140 atoms
> >  14 Water   :   600 atoms
> >  15 SOL :   600 atoms
> >  16 non-Water   :   374 atoms
> >
> > Here i need say the nitrogen present in protein (1 protein: 10 atoms)
> index
> > and the nitrogen's present in tmao (13 TMAO: 140 atoms) in the .ndx
> > file.ie.,
> > i need the nitrogen present in protein and nitrogen's present in tmao in
> > the index file..
> > How can i get this..?? wht will be the commands for this... i tried with
> > various commands but in vain
> >
> >
> > Thank you...
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> >
> >
> >
> >  Sent with Mailtrack
> >  > referral=cy16f01.di...@nitk.edu.in&idSignature=22>
> > --
> > Gromacs Users mailing list
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> > * Please search the archive at http://www.gromacs.org/
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] 5' phosphate of RNA

[mohammad fathabadi]

Thank you Justin 
I saw SOMNATH question and your answer about 5' PHO on 5 Jul. 
According that answer,  I  put PRES 5 PHO from  top_all36_na.rtf   file in 
merged.n.tdb  file after [5TER] section but I receive many errors like: Atom NA 
not found in  1GUN buiding block wile rtp and itp Atom N not found in  1GUN 
buiding block wile rtp and itp Atom C not found in  1GUN buiding block wile rtp 
and itp In my opinion I put 5 PHO patch in wrong position. where should I put 
this patch in merged.n.tdb file correctly  and it is neccesory that edit [5TER] 
section in this file.I have used CHARMM36(2017) for gromacs.Thank you for any 
advice 
Regards  


On Tuesday, June 20, 2017, 5:27:45 AM GMT+4:30, Justin Lemkul  
wrote:



On 6/19/17 8:55 AM, Mohammad fat habadi wrote:
> DEAR Users
> I have a RNA that has phosphate(P,OP,OP2,OP3) on 5’.
> IN RNA and DNA, 3’ has phosphate and 5‘ doesn’t it and for this all Force 
> fields don’t know phosphate atoms on 5’ of RNA.
> pdb2gmx  make an error.
> IF I delete 5’ phosphate atoms, I don’t have any problems.
> How can I solve this problem without deleting 5’ phosphate.

To keep the phosphate, you need to add a suitable rna.n.tdb entry in whatever 
force field you're using.  Most force fields may not support this.  CHARMM 
does, 
but it's not implemented in the GROMACS port.  You can get the parameters from 
the CHARMM force field files - look in top_all36_na.rtf (PRES 5PHO).

http://mackerell.umaryland.edu/charmm_ff.shtml#charmm

-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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[gmx-users] Error of DNA topology

[maria khan]

Dear gromacs user.

i am simulating protein having DNA ,,when i applied for pdb to gmx
command,it gives me error like  """Residue 9 named DG of a molecule in the
input file was mapped
to an entry in the topology database, but the atom O5' used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed."""

while using charmm27 all-atom ff.By using gromos 96 43a1 ff, it doesnt form
topology for DNA

kindly give me a detail answer.

thanks
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[gmx-users] Using an rtp file in an non standard directory

[Miguel Caro]

Hello,

I have created my own rtp file which I want to use in conjunction with
the OPLS force field. If I understand it correctly, the easiest way to
get pdb2gmx to build my topology would be to copy my rtp file into the
oplsaa.ff/ directory, and Gromacs looks for my molecule name inside
anything with an *rtp extension, including my rtp file. However, I have
no write permission to the oplsaa.ff/ directory of my Gromacs
installation. How can I get pdb2gmx to search inside my rtp file when
it's in a non-standard directory (e.g. in the current working directory)?

Thanks,

Miguel

-- 
*Dr. Miguel Caro*
/Postdoctoral researcher/
Department of Electrical Engineering and Automation,
and COMP Centre of Excellence in Computational Nanoscience
Aalto University, Finland
Personal email: *mcar...@gmail.com*
Work: *miguel.c...@aalto.fi*
Website: http://mcaroba.dyndns.org
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Re: [gmx-users] Using an rtp file in an non standard directory

[Mark Abraham]

Hi,

Make a copy of the whole forcefield. See
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Modifying_a_force_field

Mark

On Tue, Jul 11, 2017 at 2:51 PM Miguel Caro  wrote:

> Hello,
>
> I have created my own rtp file which I want to use in conjunction with
> the OPLS force field. If I understand it correctly, the easiest way to
> get pdb2gmx to build my topology would be to copy my rtp file into the
> oplsaa.ff/ directory, and Gromacs looks for my molecule name inside
> anything with an *rtp extension, including my rtp file. However, I have
> no write permission to the oplsaa.ff/ directory of my Gromacs
> installation. How can I get pdb2gmx to search inside my rtp file when
> it's in a non-standard directory (e.g. in the current working directory)?
>
> Thanks,
>
> Miguel
>
> --
> *Dr. Miguel Caro*
> /Postdoctoral researcher/
> Department of Electrical Engineering and Automation,
> and COMP Centre of Excellence in Computational Nanoscience
> Aalto University, Finland
> Personal email: *mcar...@gmail.com*
> Work: *miguel.c...@aalto.fi*
> Website: http://mcaroba.dyndns.org
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Re: [gmx-users] Error of DNA topology

[Mark Abraham]

Hi,

Like it says, you'll need to understand why pdb2gmx expects O5' but your
coordinate file doesn't have one. We can't see your files or understand the
context of residue 9.

Mark

On Tue, Jul 11, 2017 at 2:14 PM maria khan 
wrote:

> Dear gromacs user.
>
> i am simulating protein having DNA ,,when i applied for pdb to gmx
> command,it gives me error like  """Residue 9 named DG of a molecule in the
> input file was mapped
> to an entry in the topology database, but the atom O5' used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed."""
>
> while using charmm27 all-atom ff.By using gromos 96 43a1 ff, it doesnt form
> topology for DNA
>
> kindly give me a detail answer.
>
> thanks
> --
> Gromacs Users mailing list
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Re: [gmx-users] Help on MD performance, GPU has less load than CPU.

[Mark Abraham]

Hi,

I'm genuinely curious about why people set ewald_rtol smaller (which is
unlikely to be useful, because the accumulation of forces in single
precision will have round-off error that means the approximation to the
correct sum is not reliably accurate to more than about 1 in 1e-5), and
thus pme_order to large values - second time I've seen this in 24 hours. Is
there data somewhere that shows this is useful?

In any case, it a) causes a lot more work on the CPU, and b) only 4 (and to
a lesser extent, 5) is optimized for performance (because there's no data
that shows higher order is useful). And for free-energy calculation, that
extra expense accrues for each lambda state. See the "PME mesh" parts of
the performance report.

Guessing wildly, the cost of your simulation is probably at least double
what the defaults would give, and for that cost, I'd want to know why.

Mark

On Mon, Jul 10, 2017 at 5:02 PM Davide Bonanni 
wrote:

> Hi,
>
> I am working on a node with Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz, 16
> physical core, 32 logical core and 1 GPU NVIDIA GeForce GTX 980 Ti.
> I am launching a series of 2 ns molecolar dynamics simulations of a system
> of 6 atoms.
> I tried diverse setting combination, but however i obtained the best
> performance with the command:
>
> "gmx mdrun  -deffnm md_LIG -cpt 1 -cpo restart1.cpt -pin on"
>
> which use 32 OpenMP threads, 1 MPI thread, and the GPU.
> At the end of the file.log of molecular dynamic production I obtain this
> message:
>
> "NOTE: The GPU has >25% less load than the CPU. This imbalance causes
>   performance loss."
>
> I don't know how can improve the load on CPU more than this, or how I can
> decrease the load on GPU. Do you have any suggestions?
>
> Thank you in advance.
>
> Cheers,
>
> Davide Bonanni
>
>
> Initial and final part of LOG file here:
>
> Log file opened on Sun Jul  9 04:02:44 2017
> Host: bigblue  pid: 16777  rank ID: 0  number of ranks:  1
>:-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:
>
>
>
> GROMACS:  gmx mdrun, VERSION 5.1.4
> Executable:   /usr/bin/gmx
> Data prefix:  /usr/local/gromacs
> Command line:
>   gmx mdrun -deffnm md_fluo_7 -cpt 1 -cpo restart1.cpt -pin on
>
> GROMACS version:VERSION 5.1.4
> Precision:  single
> Memory model:   64 bit
> MPI library:thread_mpi
> OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
> GPU support:enabled
> OpenCL support: disabled
> invsqrt routine:gmx_software_invsqrt(x)
> SIMD instructions:  AVX2_256
> FFT library:fftw-3.3.4-sse2-avx
> RDTSCP usage:   enabled
> C++11 compilation:  disabled
> TNG support:enabled
> Tracing support:disabled
> Built on:   Tue  8 Nov 12:26:14 CET 2016
> Built by:   root@bigblue [CMAKE]
> Build OS/arch:  Linux 3.10.0-327.el7.x86_64 x86_64
> Build CPU vendor:   GenuineIntel
> Build CPU brand:Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
> Build CPU family:   6   Model: 63   Stepping: 2
> Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
> lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
> rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> C compiler: /bin/cc GNU 4.8.5
> C compiler flags:-march=core-avx2-Wextra
> -Wno-missing-field-initializers
> -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value
> -Wunused-parameter  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
>  -Wno-array-bounds
> C++ compiler:   /bin/c++ GNU 4.8.5
> C++ compiler flags:  -march=core-avx2-Wextra
> -Wno-missing-field-initializers
> -Wpointer-arith -Wall -Wno-unused-function  -O3 -DNDEBUG -funroll-all-loops
> -fexcess-precision=fast  -Wno-array-bounds
> Boost version:  1.55.0 (internal)
> CUDA compiler:  /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler
> driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on
> Sun_Sep__4_22:14:01_CDT_2016;Cuda compilation tools, release 8.0, V8.0.44
> CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=
> compute_30,code=sm_30;-gencode;arch=compute_35,code=
> sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=
> compute_50,code=sm_50;-gencode;arch=compute_52,code=
> sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=
> compute_61,code=sm_61;-gencode;arch=compute_60,code=
> compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;;
> ;-march=core-avx2;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-
> Wall;-Wno-unused-function;-O3;-DNDEBUG;-funroll-all-loops;-
> fexcess-precision=fast;-Wno-array-bounds;
> CUDA driver:8.0
> CUDA runtime:   8.0
>
>
> Running on 1 node with total 16 cores, 32 logical cores, 1 compatible GPU
> Hardware detected:
>   CPU info:
> Vendor: GenuineIntel
> Brand:  Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz
> Family:  6  model: 63  stepping:  2
> CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
> lahf_lm mmx msr nonstop_tsc

Re: [gmx-users] problem: gromacs run on gpu

[Mark Abraham]

Hi,

Making your run stay to the cores it is assigned is always a good idea, and
using -pin on is a good way to do it. If there's more than that job on the
node, then it is more complicated than that. More information here
http://manual.gromacs.org/documentation/2016.3/user-guide/mdrun-performance.html
.

Mark

On Sat, Jul 8, 2017 at 10:25 PM leila karami 
wrote:

> *Dear Szilárd ,*
> *Thanx for your answer. *
>
>
> *For the following command, should I use -pin on?*
>
>  gmx_mpi mdrun -nb gpu -v -deffnm  gpu_md -ntomp 32 -gpu_id 0
>
> Best wishes
> --
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Re: [gmx-users] Problem reading pdb files

[Mark Abraham]

Hi,

I imagine that at least one of the trajectories did not have a good PCA
analysis because you probably want both trajectories such that molecules
are whole with respect to PBC. The frame from the second trajectory is not.
There's a useful workflow at
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions.
Doing this means that you'll be concatenating apples to apples.

Mark

On Fri, Jul 7, 2017 at 6:52 PM Nawel Mele  wrote:

> Hi all,
>
> I have two pdb files extracted from two trajectories of same compound but
> starting from two different configurations. I wanted to combined the two
> trajectories but I faced a broken structures behaviour while combining the
> two ensembles. I just attached two first frames of each trajectories to
> show you that they seem to look fine but once you combined them and
> visualised them the second file is broken or vice versa . From that if I
> want to perform a PCA analysis I got problem to extract the PC extreme
> frames.
>
> Do you have any ideas?
> You ca try combined these two pdb files and you will understand my problem
> :(
>
> REMARKGENERATED BY TRJCONV
> TITLE  t=  -1.0
> MODEL1
> ATOM  1  S1  MOL 1  27.620  28.290  12.400  1.00
> 0.00
> ATOM  2  N1  MOL 1  28.150  27.440  11.100  1.00
> 0.00
> ATOM  3  C1  MOL 1  26.140  29.080  11.850  1.00
> 0.00
> ATOM  4  O1  MOL 1  27.210  27.410  13.450  1.00
> 0.00
> ATOM  5  O2  MOL 1  28.600  29.300  12.640  1.00
> 0.00
> ATOM  6  C2  MOL 1  28.260  23.230  11.350  1.00
> 0.00
> ATOM  7  C3  MOL 1  28.320  21.730  11.340  1.00
> 0.00
> ATOM  8  C4  MOL 1  27.040  23.890  11.180  1.00
> 0.00
> ATOM  9  C5  MOL 1  25.790  23.130  11.010  1.00
> 0.00
> ATOM 10  N2  MOL 1  24.870  23.160  12.000  1.00
> 0.00
> ATOM 11  C6  MOL 1  25.110  23.640  13.330  1.00
> 0.00
> ATOM 12  C7  MOL 1  24.070  24.700  13.670  1.00
> 0.00
> ATOM 13  C8  MOL 1  22.620  24.190  13.510  1.00
> 0.00
> ATOM 14  C9  MOL 1  23.610  22.490  11.780  1.00
> 0.00
> ATOM 15  C10 MOL 1  22.580  22.790  12.880  1.00
> 0.00
> ATOM 16  C11 MOL 1  27.000  25.290  11.090  1.00
> 0.00
> ATOM 17  C12 MOL 1  28.180  26.030  11.180  1.00
> 0.00
> ATOM 18  C13 MOL 1  29.420  25.370  11.350  1.00
> 0.00
> ATOM 19  C14 MOL 1  30.710  26.130  11.440  1.00
> 0.00
> ATOM 20  C15 MOL 1  29.450  23.970  11.440  1.00
> 0.00
> ATOM 21  O3  MOL 1  25.600  22.520   9.960  1.00
> 0.00
> ATOM 22  C16 MOL 1  20.040  26.830  11.260  1.00
> 0.00
> ATOM 23  C17 MOL 1  19.650  26.350  12.520  1.00
> 0.00
> ATOM 24  C18 MOL 1  20.490  25.480  13.210  1.00
> 0.00
> ATOM 25  C19 MOL 1  21.750  25.130  12.710  1.00
> 0.00
> ATOM 26  C20 MOL 1  22.140  25.630  11.460  1.00
> 0.00
> ATOM 27  C21 MOL 1  21.280  26.460  10.730  1.00
> 0.00
> ATOM 28  C22 MOL 1  19.140  27.610  10.450  1.00
> 0.00
> ATOM 29  N3  MOL 1  18.480  28.240   9.700  1.00
> 0.00
> TER
> ENDMDL
>
>
> REMARKGENERATED BY TRJCONV
> TITLE  t=  -1.0
> MODEL1
> ATOM  1  S1  MOL 1  21.570  24.680  12.150  1.00
> 0.00
> ATOM  2  N1  MOL 1  21.500  26.260  12.560  1.00
> 0.00
> ATOM  3  C1  MOL 1  21.600  23.930  13.730  1.00
> 0.00
> ATOM  4  O1  MOL 1  20.320  24.320  11.550  1.00
> 0.00
> ATOM  5  O2  MOL 1  22.830  24.370  11.530  1.00
> 0.00
> ATOM  6  C2  MOL 1  24.840  28.750  11.890  1.00
> 0.00
> ATOM  7  C3  MOL 1  26.060  29.580  11.620  1.00
> 0.00
> ATOM  8  C4  MOL 1  23.790  28.730  10.960  1.00
> 0.00
> ATOM  9  C5  MOL 1  22.650  27.920  11.170  1.00
> 0.00
> ATOM 10  N2  MOL 1  26.820  27.060  14.010  1.00
> 0.00
> ATOM 11  C6  MOL 1  21.560  27.870  10.130  1.00
> 0.00
> ATOM 12  C7  MOL 1  22.590  27.100  12.310  1.00
> 0.00
> ATOM 13  C8  MOL 1  23.640  27.120  13.230  1.00
> 0.00
> ATOM 14  C9  MOL 1  24.740  27.970  13.060  1.00
> 0.00
> ATOM 15  C10 MOL 1  25.800  27.960  14.110  1.00
> 0.00
> ATOM 16  C11 MOL 1  29.350  25.830  13.370  1.00
> 0.00
> ATOM 17  C12 MOL 1  28.220  25.970  12.330  1.00
> 0.00
> ATOM 18  C13 MOL 1  26.860  26.000  13.030  1.00
> 0.00
> ATOM 19  C14 MOL 1  27.820  26.940  15.040  1.00
> 0.00
> ATOM 20  C15 MOL 1  29.230  26.940  14.430  1.00
> 0.00
> ATOM 21  O3  MOL 1  25.710  28.740  15.050  1.00
> 0.00
> ATOM 22  C16 MOL 1  33.240  25.960  11.490  1.00
> 0.00
> ATOM 23  C17 MOL 1  34.620  26.190  11.130  1.00
> 0.00
> ATOM 24  C18 MOL 1  32.850  24.840  12.240  1.00
> 0.00
> ATOM   

[gmx-users] Modifying force field for graphene

[‪Mohammad Roostaie‬ ‪]

Hi All,
I want to simulate graphene by using OPLS_AA force field. Does this force field 
need any modification for graphene simulation?If yes, do you have any link 
tutorial for the modification?
Kind regards,Mohammad
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[gmx-users] DNa topology error.

[maria khan]

Thanks Mark Abraham.

i would like to share my pdb file as still i dont understand the error as
well as your answer,kindly look at this then explain it.
it cant be shared as the file is large.i checked the file in front of
residue 9,there is no DG at all .All along the chains is DA.
regards.
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[gmx-users] RDF

[Pandya, Akash]

Hi,

I want to calculate the RDF between a specific residue and a ligand molecule in 
my simulation box. Is this possible and do I have to make a special index group 
for that? If so how would I go about doing that?


Thanks,

Akash
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Re: [gmx-users] DNa topology error.

[Mark Abraham]

Hi,

pdb2gmx found a residue called DG and found an rtp entry that matched it.
It just didn't find an O5' atom within it. You should also be able to find
that residue.

Mark

On Tue, Jul 11, 2017 at 5:26 PM maria khan 
wrote:

> Thanks Mark Abraham.
>
> i would like to share my pdb file as still i dont understand the error as
> well as your answer,kindly look at this then explain it.
> it cant be shared as the file is large.i checked the file in front of
> residue 9,there is no DG at all .All along the chains is DA.
> regards.
> --
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[gmx-users] umbrella sampling

[Ben Tam]

Dear All,

I am doing umbrella sampling for a water molecules moving inside a crystal 
structure, however I am running into a problem on the output file with 
profile.xvg all value showing “nan”. This error has occurred when I reduce the 
slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for 0.2 and 
0.1, however only 0.2 has given me meaningful profile. The pull code I used is 
the following:

;Pull code
pull = yes
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = MOL
pull_group2_name = SOL
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = distance ; simple distance increase
;pull_coord1_vec = 0 0 1
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 10 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance > 0

and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I have 
tried increasing the k value to 50 and 100 with the same results.

The histogram shows many overlap, however when I use k value 100, it is only 
giving me individual single peak. Therefore can someone enlighten on what is 
going on?

Best regards,

Ben


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Re: [gmx-users] umbrella sampling

[André Farias de Moura]

I never did it myself, but generally speaking you don' t expect that there'
s a lot of room inside a crystal for any molecule to diffuse there,
especially when it comes to cross something like a crystallographic plane,
meaning that huge energy barriers should be there, leading to NaN and other
weird numerical issues.

in principle, larger force constants might help you to sample high energy
barrier, but it will be most likely a trial and error procedure until you
fine-tune the forces along the profile.

best

Andre

On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam  wrote:

> Dear All,
>
> I am doing umbrella sampling for a water molecules moving inside a crystal
> structure, however I am running into a problem on the output file with
> profile.xvg all value showing “nan”. This error has occurred when I reduce
> the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
> 0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
> code I used is the following:
>
> ;Pull code
> pull = yes
> pull_ngroups = 2
> pull_ncoords = 1
> pull_group1_name = MOL
> pull_group2_name = SOL
> pull_coord1_type = umbrella ; harmonic biasing force
> pull_coord1_geometry = distance ; simple distance increase
> ;pull_coord1_vec = 0 0 1
> pull_coord1_groups = 1 2
> pull_coord1_dim = N N Y
> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k = 10 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance > 0
>
> and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
> have tried increasing the k value to 50 and 100 with the same results.
>
> The histogram shows many overlap, however when I use k value 100, it is
> only giving me individual single peak. Therefore can someone enlighten on
> what is going on?
>
> Best regards,
>
> Ben
>
>
> --
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> * Please search the archive at http://www.gromacs.org/Support
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-- 
_

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] umbrella sampling

[Ben Tam]

Hi Andre,


Thanks for your answer. Actually I should clarify it is metal-organic-framework 
that I am working on which is a porous material. With the k value larger than 
100, the histogram become multiple sharp single peak. Furthermore when I look 
at individual 0.1nm slides, it runs completely fine without obvious anomaly. 
Therefore I am really confused why the profile.xvg become infinite or "nan".


Best regards,


Ben



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of André Farias 
de Moura 
Sent: Tuesday, July 11, 2017 17:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling

I never did it myself, but generally speaking you don' t expect that there'
s a lot of room inside a crystal for any molecule to diffuse there,
especially when it comes to cross something like a crystallographic plane,
meaning that huge energy barriers should be there, leading to NaN and other
weird numerical issues.

in principle, larger force constants might help you to sample high energy
barrier, but it will be most likely a trial and error procedure until you
fine-tune the forces along the profile.

best

Andre

On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam  wrote:

> Dear All,
>
> I am doing umbrella sampling for a water molecules moving inside a crystal
> structure, however I am running into a problem on the output file with
> profile.xvg all value showing “nan”. This error has occurred when I reduce
> the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
> 0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
> code I used is the following:
>
> ;Pull code
> pull = yes
> pull_ngroups = 2
> pull_ncoords = 1
> pull_group1_name = MOL
> pull_group2_name = SOL
> pull_coord1_type = umbrella ; harmonic biasing force
> pull_coord1_geometry = distance ; simple distance increase
> ;pull_coord1_vec = 0 0 1
> pull_coord1_groups = 1 2
> pull_coord1_dim = N N Y
> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k = 10 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance > 0
>
> and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
> have tried increasing the k value to 50 and 100 with the same results.
>
> The histogram shows many overlap, however when I use k value 100, it is
> only giving me individual single peak. Therefore can someone enlighten on
> what is going on?
>
> Best regards,
>
> Ben
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
Support - Gromacs
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--
_

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] Generating GROMACS input file from the GAMESS output file

[Justin Lemkul]

On 7/10/17 2:32 AM, 조영래 wrote:

Thank you Justin
Every time your comment helped me.

I should compare two system that are Zn_binding protein and Fe_binding
protein.

So I need force field that satisfies the following conditions.
First, force field contains two metal ion (Fe and Zn)information.
Second, force field contain metal ion binding mode amino acid information
for example cysteine (CYM) in AMBER.

However many force fields did not satisfied above conditions.
So I would like to generate *.gro *itp file for metal atoms by GAMESS.
But according to your comment this is not correct.

In my case, the metal ions (Fe and Zn) binds one cysteine and two
histidines.
I want to simulate these complexes (i.e. Fe_protein and Zn_protein complex).
Please suggest me an ideal force field that in able to be used for
sumulation of the avode mentaioned complexes.



I don't know of one.  Dealing with transition metals is one of the hardest tasks 
in parametrization.  There's a reason why after many decades of development, the 
parameters still don't exist...  Depending on what you need to do, hybrid QM/MM 
is probably the best/most straightforward approach.  Classical force fields do 
not deal well with these kinds of systems.


-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] Acetonitrile using CHARMM ff

[Justin Lemkul]

On 7/10/17 10:52 AM, Sonia Milena Aguilera Segura wrote:

Dear Justin,

Thank you for the answer. I changed the two parameters suggested in the mdp 
file and I ran again a minimization, 200 ps NVT, 200 ps NPT, and 1 ns MD for 
the two cases of the previous mail, and now I am getting densities around 771 
g/m3 which is slightly underestimated, but close to what other authors have 
obtained (774 others and 777 experimental). Also, I got slightly higher values 
for dielectric constants and diffusivities, also closer to another simulation 
with CHARMM. The energies also changed, but I guess that was expected. It looks 
like reproducing the dielectric constant with the current parameters is not 
possible. Is there anything that can be changed in order to get a better 
description? In terms of simulation, what is the dielectric constant depending 
of?



Structure, charge distribution, etc.  This may just be a limitation of an 
additive force field model.  We typically see neat liquid properties better 
reproduced with polarizable models.



Moreover, I observed that this time I got lower values for P during the NPT 
equilibration, but still is too far from 1 bar.  I really don't understand why 
for the NVT simulation I get a T around 298, but as soon as I turn on the 
pcoupl, the T rises to 300-301 K and the P gets average values of 7 and 4 bar 
(vs 8 and 14 for the previous simulations). Then at the end of the 1-ns MD the 
temperature remains around 301 and the P is -1 and 2.7 bar. Considering the 
parameters I am using, is there anything I can change to make the P coupling 
better? I am running a 3 nm box with 308 molecules. This is the full mdp file:



http://www.gromacs.org/Documentation/Terminology/Pressure

Your box is very small and will be subject to large fluctuations.

-Justin


; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.0005
nsteps   = 200   ; 1 ns
nstcomm  = 100
;energygrps  = non-Water
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme= verlet
nstlist  = 20
ns_type  = grid
pbc  = xyz
rlist= 1.2
; Electrostatics
coulombtype  = PME
rcoulomb = 1.2
; van der Waals
vdwtype  = cutoff
vdw-modifier = force-switch
rvdw-switch  = 1.0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = no
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = system
tau_t= 1.0
ref_t= 298.15
; Pressure coupling is on for NPT
Pcoupl   = Parrinello-Rahman
tau_p= 1.0
compressibility  = 4.5e-05
ref_p= 1.0
; Do not generate velocities
gen_vel  = no
; options for bonds
constraints  = none  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Constrain the starting configuration
; since we are continuing from NPT
continuation = yes
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12


Thank you very much,

Sonia Aguilera
PhD student
ENSCM

; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.0005
nsteps   = 4000   ; 20 ns
nstcomm  = 100
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme= verlet
nstlist  = 20
ns_type  = grid
pbc  = xyz
rlist= 1.2
; Electrostatics
coulombtype  = PME
rcoulomb = 1.2
; van der Waals
vdwtype  = cutoff
vdw-modifier = potential-switch
rvdw-switch  = 1.0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres


CHARMM uses a force switch, and only apply dispersion correction in the case of
lipid monolayers.

http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

-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

Re: [gmx-users] ligan minimization in vacuo

[Justin Lemkul]

On 7/10/17 5:57 PM, ‪farial tavakoli‬ ‪ wrote:

Dear gmx-users
I have a problem in equilibration my protein-ligand complex and encountered to 
this error after 2 steps of 5 steps:one or more water molecules can not be 
settled. check for bad contacts or reduce the time steps.
so I decided to create a topology for my designed drug (50 atoms) as a ligand to 
minimize it in the vacuo in the absence of the protein to check if it minimizes  , 
so i tried to change the .itp file obtained from PRODRG to create a .top file,  in 
this way:I added  " ; Include forcefield parameters
 #include "gromos43a1.ff/forcefield.itp " above the [ moleculetype ] 
directive as a first line , then added [ system ] and [ molecule ] directives under the 
ligand, respectively :
   23  24  26  27   1180.0   33.5 2180.0   33.5 2 ; dih   CAS  CAR  NAQ 
 CAN
   32  27  26  24   1180.0   33.5 2180.0   33.5 2 ; dih   CAM  CAN  NAQ 
 CAR
   39  37  36  30   1180.05.9 2180.05.9 2 ; dih   SAG  CAH  CAK 
 CAP
   40  48  49  50   1180.07.1 2180.07.1 2 ; dih   CAA  CAF  OAJ 
 HAJ

; Ligand position restraints
#ifdef POSRES
#include "posre_DRG.itp"
#endif

; Include water topology
#include "gromos43a1.ff/spc.itp"

[ system ]
; Name
DRG in water

[ molecules ]
; Compound#mols
DRG  1
issued this command:gmx grompp -v -f em.mdp -c DRG.gro -p DRG.top -o 
DRG-EM-vacuum.tprgmx mdrun -v -deffnm DRG-EM-vacuum -c DRG-EM-vacuum.gro
and simulation results:
Steepest Descents:
Tolerance (Fmax)   =  1.0e+03
Number of steps=5
Step=0, Dmax= 1.0e-02 nm, Epot=  1.41636e+03 Fmax= 2.81150e+04, atom= 25
Step=1, Dmax= 1.0e-02 nm, Epot=  1.01416e+03 Fmax= 1.21118e+04, atom= 25
Step=2, Dmax= 1.2e-02 nm, Epot=  7.87016e+02 Fmax= 4.71639e+03, atom= 25
Step=3, Dmax= 1.4e-02 nm, Epot=  6.94638e+02 Fmax= 5.88719e+03, atom= 15
Step=5, Dmax= 8.6e-03 nm, Epot=  6.79808e+02 Fmax= 7.13390e+03, atom= 15
Step=7, Dmax= 5.2e-03 nm, Epot=  6.29169e+02 Fmax= 1.31714e+03, atom= 25
Step=8, Dmax= 6.2e-03 nm, Epot=  6.12279e+02 Fmax= 2.91712e+03, atom= 14
Step=   10, Dmax= 3.7e-03 nm, Epot=  6.04849e+02 Fmax= 2.77294e+03, atom= 27
Step=   12, Dmax= 2.2e-03 nm, Epot=  5.86062e+02 Fmax= 9.77798e+02, atom= 24

writing lowest energy coordinates.

Back Off! I just backed up DRG-EM-vacuum.gro to ./#DRG-EM-vacuum.gro.1#

Steepest Descents converged to Fmax < 1000 in 13 steps
Potential Energy  =  5.8606232e+02
Maximum force =  9.7779791e+02 on atom 24
Norm of force =  3.8248090e+02

Simulation ended prematurely, no performance report will be written.


  here's my em.mdp file:

integrator  = steep; Algorithm (steep = steepest descent 
minimization)
emtol= 1000.0  ; Stop minimization when the maximum force < 
10.0 kJ/mol
emstep = 0.01 ; Energy step size
nsteps  = 5   ; Maximum number of (minimization) steps to 
perform
energygrps= system; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist   = 1; Frequency to update the neighbor list 
and long range forces
cutoff-scheme   = Verlet
ns_type= grid; Method to determine neighbor list (simple, 
grid)
rlist  = 1.0; Cut-off for making neighbor list (short 
range forces)
coulombtype = PME  ; Treatment of long range electrostatic interactions
rcoulomb  = 1.0; long range electrostatic cut-off
rvdw= 1.0; long range Van der Waals cut-off
pbc = xyz; Periodic Boundary Conditions



To minimize in vacuo, cutoffs should all be set to zero, no PBC, no PME, simple 
neighbor searching and group cutoff scheme.



I just wanted to know if I did correct?In addition after minimization in vacuo 
, checked my ligand in pymol and noticed it is disintegrated.  Is there anyone 
help me how come it is disintegrated ,however i edited the .itp file obtained 
from PRODRG ( charges and charg groups)? How can i fix this problem to 
equilibrate my complex?


You'll have to define "disintegrated" because bonds can't break or form in 
classical molecular mechanical processes, so perhaps PyMOL is just having a hard 
time guessing the bonded structure.  You have to be judicious in what 
modifications you make to the topology.  PRODRG topologies require complete 
reparametrization of (at least) the charges, but without knowing what you did or 
why you did it, there's little to go on here.


-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://ma

Re: [gmx-users] Concrete pull code explanation needed

[Justin Lemkul]

On 7/10/17 11:19 PM, Du, Yu wrote:

Dear Justin and gmx users,


I have gone through mdp-option and Justin A. Lemkul's COM pulling tutorial 
serveral times.


The following is Justin's pull code.


; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= Chain_B
pull_group2_name= Chain_A
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups= 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0


My understanding lists as follows,


Justin defines two pull groups, with `pull-ngroups = 2`, each of them has a 
name in the index.ndx generated by `gmx make_ndx -f npt.gro`and their names are 
defined by `pull_group1_name = Chain_B` and `pull_group2_name = Chain_A`.


My question is about the definition of pulling coordination and the orientation 
of pulling force.


1) I learnt from [gmx-users] Change to umbrella sampling pull code，
"You need: pull-coord1-groups = 1 2 otherwise the reaction coordinate is undefined, 
or otherwise defaults to the entire system, I can't remember which. -Justin"


I know it's a plot :) in the input.pdb that proteins are placed exquisitely 
along the z-axis which is the same as the pulling coordinate but it makes pull 
code confused and here I need a concrete explanation.
1.The pull coordinate is the line that connects COM of group1 and group2 with 
`pull_coord1_groups= 1 2`.
OR 2. The pull coordinate is the z axis with `pull_coord1_dim = N N Y`.
Which is correct?



The z-component of the vector connecting the COMs of the two groups.



2)Then turn to the orientation of pulling forces.
My understanding is that force1 acts on pull_group1, force2 acts on pull_group2 
and the orientation of force 1 and 2 is opposite, both forces have a rate of 
10nm per ns.
Is my understanding and the below schematic draw right?



There is one force.  It acts on the spring connecting the two groups.



Z-axis-0-5--->---positive-orientation--->-25-->



The last question is about the umbrella sampling.
I learnt from [gmx-users] Re: doubt about your Umbrella Sampling tutorial that 
it's ok to remove the pores of Chain B during the US. But in longer simulation 
time and in the periodical box, will the COM of Chain B and A be affacted by 
the boundary? and then affact the calculation of US potential?



The tutorial system won't work if you turn off the restraint.  Eventually the 
system will rotate and the groups will cross periodic boundaries, which will 
cause the chosen pull geometry to fail.  So the restraints serve a dual purpose: 
(1) to mimic the stability of larger amyloid assemblies and (2) to reduce the 
system size, as several hundred thousand atoms was not feasible for me at the time.


-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] Using CHARMM36 in GROMACS to simulate polysaccharides

[Justin Lemkul]

On 7/11/17 2:46 AM, Akash Ranjan wrote:

Sir,

I am facing difficulty in making topology for a simple molecule using CHARMM36 
but i am facing certain difficulty in that such as


(a)Warning: Long Bond (3-10 = 0.566378 nm)
Warning: Long Bond (3-4 = 0.426475 nm)
Warning: Long Bond (4-16 = 0.59 nm)
Warning: Long Bond (4-11 = 0.671583 nm)
Warning: Long Bond (5-6 = 0.428864 nm)
Warning: Short Bond (5-7 = 0.044 nm)
Warning: Long Bond (7-8 = 0.648229 nm)
Warning: Long Bond (8-20 = 0.539527 nm)
Warning: Long Bond (9-21 = 0.849567 nm)
Warning: Long Bond (10-22 = 0.584145 nm)
Warning: Long Bond (11-23 = 0.637749 nm)


(b)
ERROR 4 [file topol.top, line 76]:
   No default Bond types




ERROR 7 [file topol.top, line 169]:
   No default U-B types


ERROR 19 [file topol.top, line 202]:
   No default Proper Dih. types



The missing parameters mean your atom type assignments are incorrect.


Here is mine rtp enteries.can you suggest me how to correct t?


[ UNK ]
   [ atoms ]
C1 CC3161   12.01100 1
C2 CC3161   12.01100 2
C3 CC3161   12.01100 3
C4 CC3162   12.01100 4
C5 CC3163   12.01100 5
O6 OC3C61   -0.400   6
C7 CC3161   12.01100 7
O8 OC311-0.650   8
O9 OC311-0.650   9
   O10 OC311-0.650   10
   O11 OC311-0.650   11
   O12 OC311-0.650   12
   H13 HCA1 1.00800  13
   H14 HCA1 1.00800  14
   H15 HCA1 1.00800  15
   H16 HCA1 1.00800  16
   H17 HCA1 1.00800  17
   H18 HCA1 1.00800  18
   H19 HCA1 1.00800  19
   H20 HX   0.09020
   H21 HX   0.09021
   H22 HX   0.09022
   H23 HX   0.09023
   H24 HX   0.09024



You have a mix of charges and masses in the column that should only be charges, 
so this is a fundamentally broken entry.




   [ bonds ]
C1H13
C1O12
C1C5
C1C2
C2H14
C2O9
C2C3
C3H15
C3O10
C3C4
C4H16
C4O11
C4O6
C5O6
C5C7
C5H17
C7H18
C7H19
C7O8
O8H20
O9H21
O10   H22
O11   H23
O12   H24

PDB file:-



Have you visualized these coordinates?  The format is totally broken so this is 
what pdb2gmx is complaining about.  The structure is complete nonsense.


-Justin


HEADERPROTEIN 06-JUL-17   NONE
TITLE NULL
COMPNDMOLECULE: ads1.mol
SOURCENULL
KEYWDSNULL
EXPDTANULL
AUTHORMarvin
ATOM  1  C1   UNK 0   2.462  -3.244   0.792  1.00  0.00   C
ATOM  2  C2   UNK 0   2.766  -4.727   0.446  1.00  0.00   C
ATOM  3  C3   UNK 0   1.464  -5.574   0.403  1.00  0.00   C
ATOM  4  C4   UNK 0   0.378  -4.893  -0.473  1.00  0.00   C
ATOM  5  C5   UNK 0   1.343  -2.682  -0.137  1.00  0.00   C
ATOM  6  O6   UNK 0   0.167  -3.523  -0.076  1.00  0.00   O
ATOM  7  C7   UNK 0   0.903  -1.252   0.257  1.00  0.00   C
ATOM  8  O8   UNK 0  -0.118  -0.796  -0.628  1.00  0.00   O
ATOM  9  O9   UNK 0   3.663  -5.266   1.418  1.00  0.00   O
ATOM 10  O10  UNK 0   1.748  -6.880  -0.095  1.00  0.00   O
ATOM 11  O11  UNK 0   0.692  -4.976  -1.864  1.00  0.00   O
ATOM 12  O12  UNK 0   3.652  -2.465   0.678  1.00  0.00   O
HETATM   13  H13  UNK 0   2.111  -3.189   1.801  1.00  0.00   H
HETATM   14  H14  UNK 0   3.215  -4.763  -0.524  1.00  0.00   H
HETATM   15  H15  UNK 0   1.084  -5.651   1.400  1.00  0.00   H
HETATM   16  H16  UNK 0  -0.535  -5.428  -0.314  1.00  0.00   H
HETATM   17  H17  UNK 0   1.761  -2.663  -1.122  1.00  0.00   H
HETATM   18  H18  UNK 0   1.744  -0.593   0.198  1.00  0.00   H
HETATM   19  H19  UNK 0   0.522  -1.264   1.257  1.00  0.00   H
HETATM   20  H20  UNK 0   0.223  -0.784  -1.536  1.00  0.00   H
HETATM   21  H21  UNK 0   3.249  -5.230   2.295  1.00  0.00   H
HETATM   22  H22  UNK 0   2.093  -6.813  -0.999  1.00  0.00   H
HETATM   23  H23  UNK 0   1.518  -4.498  -2.038  1.00  0.00   H
HETATM   24  H24  UNK 0   3.980  -2.507  -0.234  1.00  0.00   H
CONECT125   12   13
CONECT2139   14
CONECT324   10   15
CONECT436   11   16
CONECT5167   17
CONECT645
CONECT758   18   19
CONECT8

Re: [gmx-users] 5' phosphate of RNA

[Justin Lemkul]

On 7/11/17 7:06 AM, mohammad fathabadi wrote:

Thank you Justin
I saw SOMNATH question and your answer about 5' PHO on 5 Jul.
According that answer,  I  put PRES 5 PHO from  top_all36_na.rtf   file in 
merged.n.tdb  file after [5TER] section but I receive many errors like: Atom NA 
not found in  1GUN buiding block wile rtp and itp Atom N not found in  1GUN 
buiding block wile rtp and itp Atom C not found in  1GUN buiding block wile rtp 
and itp In my opinion I put 5 PHO patch in wrong position. where should I put 
this patch in merged.n.tdb file correctly  and it is neccesory that edit [5TER] 
section in this file.I have used CHARMM36(2017) for gromacs.Thank you for any 
advice


I don't know what residue "GUN" is, but it looks like pdb2gmx is trying to treat 
it as a protein, which means you didn't add it correctly as an entry in 
residuetypes.dat.  Beyond that, I can't comment on how you might have 
implemented the patch, so you'll have to provide more details.


-Justin


Regards


On Tuesday, June 20, 2017, 5:27:45 AM GMT+4:30, Justin Lemkul  
wrote:



On 6/19/17 8:55 AM, Mohammad fat habadi wrote:

DEAR Users
I have a RNA that has phosphate(P,OP,OP2,OP3) on 5’.
IN RNA and DNA, 3’ has phosphate and 5‘ doesn’t it and for this all Force 
fields don’t know phosphate atoms on 5’ of RNA.
pdb2gmx  make an error.
IF I delete 5’ phosphate atoms, I don’t have any problems.
How can I solve this problem without deleting 5’ phosphate.


To keep the phosphate, you need to add a suitable rna.n.tdb entry in whatever
force field you're using.  Most force fields may not support this.  CHARMM does,
but it's not implemented in the GROMACS port.  You can get the parameters from
the CHARMM force field files - look in top_all36_na.rtf (PRES 5PHO).

http://mackerell.umaryland.edu/charmm_ff.shtml#charmm

-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] Modifying force field for graphene

[Justin Lemkul]

On 7/11/17 10:34 AM, ‪Mohammad Roostaie‬ ‪ wrote:

Hi All,
I want to simulate graphene by using OPLS_AA force field. Does this force field 
need any modification for graphene simulation?If yes, do you have any link 
tutorial for the modification?


What do you find when investigating the literature on the use of OPLS for 
graphene simulations?


-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] RDF

[Justin Lemkul]

On 7/11/17 11:41 AM, Pandya, Akash wrote:

Hi,

I want to calculate the RDF between a specific residue and a ligand molecule in 
my simulation box. Is this possible and do I have to make a special index group 
for that? If so how would I go about doing that?



By using make_ndx or a suitable command-line selection when running gmx rdf (see 
gmx help selections, but make_ndx is often much easier to use/comprehend for 
very simple cases like this).


-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] umbrella sampling

[Justin Lemkul]

On 7/11/17 12:53 PM, Ben Tam wrote:

Hi Andre,


Thanks for your answer. Actually I should clarify it is metal-organic-framework that I am working on which is a porous material. With the k value larger than 100, the histogram become multiple sharp single peak. 
Furthermore when I look at individual 0.1nm slides, it runs completely fine 
without obvious anomaly. Therefore I am really confused why the profile.xvg 
become infinite or "nan".




I'm really confused about your setup.  From what it sounds like, your windows 
are too narrow to get good sampling, perhaps the force constant is too strong, 
and I'm really not sure why you're only applying a restraint along z.  What is 
the geometry of your system?  Don't follow my tutorial too closely, it's not 
appropriate for most cases...


-Justin



Best regards,


Ben



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of André Farias de 
Moura 
Sent: Tuesday, July 11, 2017 17:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling

I never did it myself, but generally speaking you don' t expect that there'
s a lot of room inside a crystal for any molecule to diffuse there,
especially when it comes to cross something like a crystallographic plane,
meaning that huge energy barriers should be there, leading to NaN and other
weird numerical issues.

in principle, larger force constants might help you to sample high energy
barrier, but it will be most likely a trial and error procedure until you
fine-tune the forces along the profile.

best

Andre

On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam  wrote:


Dear All,

I am doing umbrella sampling for a water molecules moving inside a crystal
structure, however I am running into a problem on the output file with
profile.xvg all value showing “nan”. This error has occurred when I reduce
the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
code I used is the following:

;Pull code
pull = yes
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = MOL
pull_group2_name = SOL
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = distance ; simple distance increase
;pull_coord1_vec = 0 0 1
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 10 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance > 0

and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
have tried increasing the k value to 50 and 100 with the same results.

The histogram shows many overlap, however when I use k value 100, it is
only giving me individual single peak. Therefore can someone enlighten on
what is going on?

Best regards,

Ben


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Re: [gmx-users] umbrella sampling

[Ben Tam]

Hi Justin,


I am trying to get an energy profile when water molecules go through the porous 
cage. I am restraint it to z direction because I would like to see the energy 
that require to jump from one cage to another. I set up the simulation so that 
the structure is repeated at z direction which this will give me more sample 
slice for starting configuration. Sorry I am still new to the umbrella sampling.


Best regards,


Ben





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

Sent: Tuesday, July 11, 2017 18:07
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling



On 7/11/17 12:53 PM, Ben Tam wrote:
> Hi Andre,
>
>
> Thanks for your answer. Actually I should clarify it is 
> metal-organic-framework that I am working on which is a porous material. With 
> the k value larger than 100, the histogram become multiple sharp single peak.
Furthermore when I look at individual 0.1nm slides, it runs completely fine
without obvious anomaly. Therefore I am really confused why the profile.xvg
become infinite or "nan".
>

I'm really confused about your setup.  From what it sounds like, your windows
are too narrow to get good sampling, perhaps the force constant is too strong,
and I'm really not sure why you're only applying a restraint along z.  What is
the geometry of your system?  Don't follow my tutorial too closely, it's not
appropriate for most cases...

-Justin

>
> Best regards,
>
>
> Ben
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of André Farias 
> de Moura 
> Sent: Tuesday, July 11, 2017 17:44
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] umbrella sampling
>
> I never did it myself, but generally speaking you don' t expect that there'
> s a lot of room inside a crystal for any molecule to diffuse there,
> especially when it comes to cross something like a crystallographic plane,
> meaning that huge energy barriers should be there, leading to NaN and other
> weird numerical issues.
>
> in principle, larger force constants might help you to sample high energy
> barrier, but it will be most likely a trial and error procedure until you
> fine-tune the forces along the profile.
>
> best
>
> Andre
>
> On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam  wrote:
>
>> Dear All,
>>
>> I am doing umbrella sampling for a water molecules moving inside a crystal
>> structure, however I am running into a problem on the output file with
>> profile.xvg all value showing “nan”. This error has occurred when I reduce
>> the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
>> 0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
>> code I used is the following:
>>
>> ;Pull code
>> pull = yes
>> pull_ngroups = 2
>> pull_ncoords = 1
>> pull_group1_name = MOL
>> pull_group2_name = SOL
>> pull_coord1_type = umbrella ; harmonic biasing force
>> pull_coord1_geometry = distance ; simple distance increase
>> ;pull_coord1_vec = 0 0 1
>> pull_coord1_groups = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
>> pull_coord1_k = 10 ; kJ mol^-1 nm^-2
>> pull_coord1_start = yes ; define initial COM distance > 0
>>
>> and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
>> have tried increasing the k value to 50 and 100 with the same results.
>>
>> The histogram shows many overlap, however when I use k value 100, it is
>> only giving me individual single peak. Therefore can someone enlighten on
>> what is going on?
>>
>> Best regards,
>>
>> Ben
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support

> Support - Gromacs

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> your GROMACS version number (and if it's not the most recent, try installing 
> that first!),
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Re: [gmx-users] RDF

[Pandya, Akash]

When I try to make an index group for the protein residue and the ligand 
molecule, the whole system is included in the index file. 

I use these options:

r 166 (protein residue)

r 901 (ligand molecule)

then press q

Akash 

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: 11 July 2017 18:06
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] RDF



On 7/11/17 11:41 AM, Pandya, Akash wrote:
> Hi,
> 
> I want to calculate the RDF between a specific residue and a ligand molecule 
> in my simulation box. Is this possible and do I have to make a special index 
> group for that? If so how would I go about doing that?
> 

By using make_ndx or a suitable command-line selection when running gmx rdf 
(see gmx help selections, but make_ndx is often much easier to use/comprehend 
for very simple cases like this).

-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] Modifying force field for graphene

[Alex]

The answer is yes, OPLSAA does need to be slightly edited for graphene 
and nanotubes to work, assuming you find good parameters for graphene. 
Google is strong with you, use it.


Alex

On 7/11/2017 8:34 AM, ‪Mohammad Roostaie‬ ‪ wrote:

Hi All,
I want to simulate graphene by using OPLS_AA force field. Does this force field 
need any modification for graphene simulation?If yes, do you have any link 
tutorial for the modification?
Kind regards,Mohammad


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[gmx-users] DNA topology error

[maria khan]

dear Mark Abraham

According to my error like  """Residue 9 named DG of a molecule in the
input file was mapped to an entry in the topology database, but the atom
O5' used in that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed."""

if O5' can be set in pdb manually,then how  the other values of
cordinates   (figures) can be provided manually,as these values are
experimental.

Thanks.

Maria.
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[gmx-users] output pdb reformatted

[Alex]

Hi all,

I have a tiny acetonitrile molecule here. The input pdb prior to EM is this:

TITLE Gromacs Runs On Most of All Computer Systems
REMARKTHIS IS A SIMULATION BOX
CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1
MODEL1
ATOM  1  CT  ACT 1  14.870  14.744  14.594  1.00  0.00
  C
ATOM  2  HC  ACT 1  15.390  13.760  14.594  1.00  0.00
  H
ATOM  3  HC  ACT 1  13.769  14.581  14.594  1.00  0.00
  H
ATOM  4  HC  ACT 1  15.162  15.317  13.685  1.00  0.00
  H
ATOM  5  CZ  ACT 1  15.253  15.501  15.794  1.00  0.00
  C
ATOM  6  NZ  ACT 1  15.555  16.097  16.740  1.00  0.00
  N
TER
ENDMDL

The output, however, is this:

TITLE Great Red Owns Many ACres of Sand
REMARKTHIS IS A SIMULATION BOX
CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1   1
MODEL1
ATOM  1  1CT 1  15.013  15.013  14.819  1.00  0.00
  C
ATOM  2  1HC 1  14.952  13.831  14.385  1.00  0.00
  H
ATOM  3  1HC 1  13.827  14.934  14.400  1.00  0.00
  H
ATOM  4  1HC 1  15.140  15.157  13.573  1.00  0.00
  H
ATOM  5  2CZ 1  15.821  15.819  16.308  1.00  0.00
  C
ATOM  6  2NZ 1  16.401  16.397  17.446  1.00  0.00
  N
TER
ENDMDL

Why? I don't think I've seen this happen before, and I'd like to keep the
initial format. Any suggestions? My itp is for an ACT residue, which is
included in the simulation topology input.

Thank you,

Alex
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[gmx-users] Gmx 2016.3 compilation error on PHI

[Jones de Andrade]

Hi all.

I'm having some issues while trying to compile the Gromacs 2016.3 version
for a Xeon Phi Knights *Corner* (not Landing).

I'm running the latest version of cmake (own compilation, worked on other
compilations done previously: 5.1.2 on gcc and 2016.3 on gcc and icc) with
the following line at the moment (sorry for the long paths):

*
/home/jdandrade/bin/bin/cmake .. -DCMAKE_C_COMPILER=icc
-DCMAKE_CXX_COMPILER=icc -DGMX_FFT_LIBRARY=mkl
-DMKL_LIBRARIES=”/opt/intel/compilers_and_libraries_2016.1.150/linux/compiler/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2016.1.150/linux/mkl/lib/intel64_lin_mic/”
-DMKL_INCLUDE_DIR=”/opt/intel/compilers_and_libraries_2016.1.150/linux/compiler/include/mic:/opt/intel/compilers_and_libraries_2016.1.150/linux/compiler/include/intel64”
-DCMAKE_INSTALL_PREFIX=/home/jdandrade/bin -DGMX_BUILD_SHARED_EXE=OFF
-DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/opt/versatushpc/compilers/gnu/5.3/lib64/
-L/opt/versatushpc/compilers/gnu/5.3/lib64/"
-DCMAKE_TOOLCHAIN_FILE=Platform/XeonPhi -DGMX_DEFAULT_SUFFIX=OFF
-DGMX_BINARY_SUFFIX=_phi -DGMX_LIBS_SUFFIX=_phi -DGMX_BUILD_MDRUN_ONLY=ON
-DCMAKE_C_FLAGS="-O3 -qopenmp -parallel -ip -mmic" -DCMAKE_CXX_FLAGS="-O3
-qopenmp -parallel -ip -mmic" -DGMX_GPU=OFF
*

It prepares the compilation fine. When I execute the "make" command it goes
all the way down to 100%, but when it comes to final linking it issues the
following errors:

*
[100%] Built target mdrun_objlib
Scanning dependencies of target mdrun
[100%] Building CXX object
src/programs/CMakeFiles/mdrun.dir/mdrun_main.cpp.o
[100%] Linking CXX executable ../../bin/mdrun_phi
x86_64-k1om-linux-ld: skipping incompatible
/opt/versatushpc/compilers/gnu/5.3/lib64//libcilkrts.so when searching for
-lcilkrts
x86_64-k1om-linux-ld: skipping incompatible
/opt/versatushpc/compilers/gnu/5.3/lib64//libcilkrts.a when searching for
-lcilkrts
x86_64-k1om-linux-ld: skipping incompatible
/opt/versatushpc/compilers/gnu/5.3/lib64//libcilkrts.so.5 when searching
for libcilkrts.so.5
x86_64-k1om-linux-ld: skipping incompatible
/opt/versatushpc/compilers/gnu/5.3/lib64//libstdc++.so when searching for
-lstdc++
x86_64-k1om-linux-ld: skipping incompatible
/opt/versatushpc/compilers/gnu/5.3/lib64//libgcc_s.so when searching for
-lgcc_s
x86_64-k1om-linux-ld: skipping incompatible
/opt/versatushpc/compilers/gnu/5.3/lib64//libgcc_s.so when searching for
-lgcc_s
*

As a consequence, when I try to execute the command, using:

gmx grompp -f 1000.BMIm.AlCl4.md.001.mdp -c 1000.BMIm.AlCl4.md.000.gro -p
1000.BMIm.AlCl4.md.top -o 1000.BMIm.AlCl4.md.001.tpr

/usr/bin/micnativeloadex mdrun_phi -a "-nt 32 -ntomp 0 -pin on -s
1000.BMIm.AlCl4.md.001.tpr -o 1000.BMIm.AlCl4.md.001.trr -x
1000.BMIm.AlCl4.md.001.xtc -c 1000.BMIm.AlCl4.md.001.gro -e
1000.BMIm.AlCl4.md.001.edr -g 1000.BMIm.AlCl4.md.001.log -cpo
1000.BMIm.AlCl4.md.001.cpt -nice 0 -v"

I get the following error message:

**
Dependency information for /home/jdandrade/bin/bin/mdrun_phi

Full path was resolved as
/home/jdandrade/bin/bin/mdrun_phi

Binary was built for Intel(R) Xeon Phi(TM) Coprocessor
(codename: Knights Corner) architecture

SINK_LD_LIBRARY_PATH =
/opt/intel/compilers_and_libraries_2016.1.150/linux/compiler/lib/intel64_lin_mic/

Dependencies Found:

/opt/intel/compilers_and_libraries_2016.1.150/linux/compiler/lib/intel64_lin_mic/libiomp5.so

Dependencies Not Found Locally (but may exist already on the
coprocessor):
libmkl_intel_lp64.so
libmkl_sequential.so
libmkl_core.so
librt.so.1
libm.so.6
libpthread.so.0
libc.so.6
libdl.so.2
libstdc++.so.6
libgcc_s.so.1
**

Does anybody has any idea on how to solve this? I would really like to give
phi a try and bench it on my systems.

Thanks a lot in advance.

Jones
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Re: [gmx-users] umbrella sampling

[Justin Lemkul]

On 7/11/17 1:38 PM, Ben Tam wrote:

Hi Justin,


I am trying to get an energy profile when water molecules go through the porous 
cage. I am restraint it to z direction because I would like to see the energy 
that require to jump from one cage to another. I set up the simulation so that 
the structure is repeated at z direction which this will give me more sample 
slice for starting configuration. Sorry I am still new to the umbrella sampling.



OK, I see what you're doing now.  That should be fine, but without seeing the 
histograms it's impossible to know how well things are working.  If you're 
getting NaN somewhere, that means a gap in the sampling.


-Justin



Best regards,


Ben





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

Sent: Tuesday, July 11, 2017 18:07
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] umbrella sampling



On 7/11/17 12:53 PM, Ben Tam wrote:

Hi Andre,


Thanks for your answer. Actually I should clarify it is metal-organic-framework 
that I am working on which is a porous material. With the k value larger than 
100, the histogram become multiple sharp single peak.

Furthermore when I look at individual 0.1nm slides, it runs completely fine
without obvious anomaly. Therefore I am really confused why the profile.xvg
become infinite or "nan".




I'm really confused about your setup.  From what it sounds like, your windows
are too narrow to get good sampling, perhaps the force constant is too strong,
and I'm really not sure why you're only applying a restraint along z.  What is
the geometry of your system?  Don't follow my tutorial too closely, it's not
appropriate for most cases...

-Justin



Best regards,


Ben



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of André Farias de 
Moura 
Sent: Tuesday, July 11, 2017 17:44
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] umbrella sampling

I never did it myself, but generally speaking you don' t expect that there'
s a lot of room inside a crystal for any molecule to diffuse there,
especially when it comes to cross something like a crystallographic plane,
meaning that huge energy barriers should be there, leading to NaN and other
weird numerical issues.

in principle, larger force constants might help you to sample high energy
barrier, but it will be most likely a trial and error procedure until you
fine-tune the forces along the profile.

best

Andre

On Tue, Jul 11, 2017 at 1:09 PM, Ben Tam  wrote:


Dear All,

I am doing umbrella sampling for a water molecules moving inside a crystal
structure, however I am running into a problem on the output file with
profile.xvg all value showing “nan”. This error has occurred when I reduce
the slide width from 0.2 nm to 0.1 nm. I have used the exact pull code for
0.2 and 0.1, however only 0.2 has given me meaningful profile. The pull
code I used is the following:

;Pull code
pull = yes
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = MOL
pull_group2_name = SOL
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = distance ; simple distance increase
;pull_coord1_vec = 0 0 1
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 10 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance > 0

and the time step I used is 500 ps, but I have also tried 100 and 50 ps. I
have tried increasing the k value to 50 and 100 with the same results.

The histogram shows many overlap, however when I use k value 100, it is
only giving me individual single peak. Therefore can someone enlighten on
what is going on?

Best regards,

Ben


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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] RDF

[Justin Lemkul]

On 7/11/17 1:38 PM, Pandya, Akash wrote:

When I try to make an index group for the protein residue and the ligand 
molecule, the whole system is included in the index file.

I use these options:

r 166 (protein residue)

r 901 (ligand molecule)

then press q



All the default groups will still be there, you're just adding new ones into the 
list that you can choose from.  Neither of those will correspond to the whole 
system, so they should be viable choices at the gmx rdf prompt.


-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] DNA topology error

[Justin Lemkul]

On 7/11/17 3:40 PM, maria khan wrote:

dear Mark Abraham

According to my error like  """Residue 9 named DG of a molecule in the
input file was mapped to an entry in the topology database, but the atom
O5' used in that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed."""

if O5' can be set in pdb manually,then how  the other values of
cordinates   (figures) can be provided manually,as these values are
experimental.



Regular B-form DNA has a predictable structure.  If yours is incomplete, there 
are a variety of utilities that you can use to model in the missing atoms.  Just 
Google around.


-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] output pdb reformatted

[Justin Lemkul]

On 7/11/17 4:01 PM, Alex wrote:

Hi all,

I have a tiny acetonitrile molecule here. The input pdb prior to EM is this:

TITLE Gromacs Runs On Most of All Computer Systems
REMARKTHIS IS A SIMULATION BOX
CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1
MODEL1
ATOM  1  CT  ACT 1  14.870  14.744  14.594  1.00  0.00
   C
ATOM  2  HC  ACT 1  15.390  13.760  14.594  1.00  0.00
   H
ATOM  3  HC  ACT 1  13.769  14.581  14.594  1.00  0.00
   H
ATOM  4  HC  ACT 1  15.162  15.317  13.685  1.00  0.00
   H
ATOM  5  CZ  ACT 1  15.253  15.501  15.794  1.00  0.00
   C
ATOM  6  NZ  ACT 1  15.555  16.097  16.740  1.00  0.00
   N
TER
ENDMDL

The output, however, is this:

TITLE Great Red Owns Many ACres of Sand
REMARKTHIS IS A SIMULATION BOX
CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1   1
MODEL1
ATOM  1  1CT 1  15.013  15.013  14.819  1.00  0.00
   C
ATOM  2  1HC 1  14.952  13.831  14.385  1.00  0.00
   H
ATOM  3  1HC 1  13.827  14.934  14.400  1.00  0.00
   H
ATOM  4  1HC 1  15.140  15.157  13.573  1.00  0.00
   H
ATOM  5  2CZ 1  15.821  15.819  16.308  1.00  0.00
   C
ATOM  6  2NZ 1  16.401  16.397  17.446  1.00  0.00
   N
TER
ENDMDL

Why? I don't think I've seen this happen before, and I'd like to keep the
initial format. Any suggestions? My itp is for an ACT residue, which is
included in the simulation topology input.



mdrun gets the residue and atom names from the topology, so a dump of the .tpr 
should show something useful.  It seems like something in the topology has 
gotten broken - atom names becoming numbers, residue name becoming the atom 
names.  Bizarre.  grompp should have complained loudly if there were mismatches 
between coordinates and topology.


-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] output pdb reformatted

[Alex]

You are absolutely right once again. I've been glancing over that topology,
looking right at what the problem was, and not seeing it. The residue name
column was empty, all atom types went to crap, but because I always grompp
with -maxwarn 10 (for completely unrelated warnings in completely different
simulations) everything seemed okay.

Thanks!

Alex

On Tue, Jul 11, 2017 at 2:40 PM, Justin Lemkul  wrote:

>
>
> On 7/11/17 4:01 PM, Alex wrote:
>
>> Hi all,
>>
>> I have a tiny acetonitrile molecule here. The input pdb prior to EM is
>> this:
>>
>> TITLE Gromacs Runs On Most of All Computer Systems
>> REMARKTHIS IS A SIMULATION BOX
>> CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1
>> MODEL1
>> ATOM  1  CT  ACT 1  14.870  14.744  14.594  1.00  0.00
>>C
>> ATOM  2  HC  ACT 1  15.390  13.760  14.594  1.00  0.00
>>H
>> ATOM  3  HC  ACT 1  13.769  14.581  14.594  1.00  0.00
>>H
>> ATOM  4  HC  ACT 1  15.162  15.317  13.685  1.00  0.00
>>H
>> ATOM  5  CZ  ACT 1  15.253  15.501  15.794  1.00  0.00
>>C
>> ATOM  6  NZ  ACT 1  15.555  16.097  16.740  1.00  0.00
>>N
>> TER
>> ENDMDL
>>
>> The output, however, is this:
>>
>> TITLE Great Red Owns Many ACres of Sand
>> REMARKTHIS IS A SIMULATION BOX
>> CRYST1   30.000   30.000   30.000  90.00  90.00  90.00 P 1   1
>> MODEL1
>> ATOM  1  1CT 1  15.013  15.013  14.819  1.00  0.00
>>C
>> ATOM  2  1HC 1  14.952  13.831  14.385  1.00  0.00
>>H
>> ATOM  3  1HC 1  13.827  14.934  14.400  1.00  0.00
>>H
>> ATOM  4  1HC 1  15.140  15.157  13.573  1.00  0.00
>>H
>> ATOM  5  2CZ 1  15.821  15.819  16.308  1.00  0.00
>>C
>> ATOM  6  2NZ 1  16.401  16.397  17.446  1.00  0.00
>>N
>> TER
>> ENDMDL
>>
>> Why? I don't think I've seen this happen before, and I'd like to keep the
>> initial format. Any suggestions? My itp is for an ACT residue, which is
>> included in the simulation topology input.
>>
>>
> mdrun gets the residue and atom names from the topology, so a dump of the
> .tpr should show something useful.  It seems like something in the topology
> has gotten broken - atom names becoming numbers, residue name becoming the
> atom names.  Bizarre.  grompp should have complained loudly if there were
> mismatches between coordinates and topology.
>
> -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] Concrete pull code explanation needed

[Du, Yu]

> On 7/10/17 11:19 PM, Du, Yu wrote:
> > Dear Justin and gmx users,
> > 
> > 
> > I have gone through mdp-option and Justin A. Lemkul's COM pulling tutorial 
> > serveral times.
> > 
> > 
> > The following is Justin's pull code.
> > 
> > 
> > ; Pull code
> > pull= yes
> > pull_ngroups= 2
> > pull_ncoords= 1
> > pull_group1_name= Chain_B
> > pull_group2_name= Chain_A
> > pull_coord1_type= umbrella  ; harmonic biasing force
> > pull_coord1_geometry= distance  ; simple distance increase
> > pull_coord1_groups= 1 2
> > pull_coord1_dim = N N Y
> > pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm per ns
> > pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
> > pull_coord1_start   = yes   ; define initial COM distance > 0
> > 
> > 
> > My understanding lists as follows,
> > 
> > 
> > Justin defines two pull groups, with `pull-ngroups = 2`, each of them has a 
> > name in the index.ndx generated by `gmx make_ndx -f npt.gro`and their names 
> > are defined by `pull_group1_name = Chain_B` and `pull_group2_name = 
> > Chain_A`.
> > 
> > 
> > My question is about the definition of pulling coordination and the 
> > orientation of pulling force.
> > 
> > 
> > 1) I learnt from [gmx-users] Change to umbrella sampling pull code，
> > "You need: pull-coord1-groups = 1 2 otherwise the reaction coordinate is 
> > undefined, or otherwise defaults to the entire system, I can't remember 
> > which. -Justin"
> > 
> > 
> > I know it's a plot :) in the input.pdb that proteins are placed exquisitely 
> > along the z-axis which is the same as the pulling coordinate but it makes 
> > pull code confused and here I need a concrete explanation.
> > 1.The pull coordinate is the line that connects COM of group1 and group2 
> > with `pull_coord1_groups= 1 2`.
> > OR 2. The pull coordinate is the z axis with `pull_coord1_dim = N N Y`.
> > Which is correct?
> > 
> 
> The z-component of the vector connecting the COMs of the two groups.
> 
> > 
> > 2)Then turn to the orientation of pulling forces.
> > My understanding is that force1 acts on pull_group1, force2 acts on 
> > pull_group2 and the orientation of force 1 and 2 is opposite, both forces 
> > have a rate of 10nm per ns.
> > Is my understanding and the below schematic draw right?
> > 
> 
> There is one force.  It acts on the spring connecting the two groups.


How does the spring connect the two groups? Does the spring link to the COM of 
the whole two groups? 
How does Gromacs define the orientation of the force of pulling? Or by default 
is the pulling force just positive along the z axis with `pull_coord1_geometry 
= distance` and `pull_coord1_dim = N N Y`?

> 
> > 
> > Z-axis-0-5--->---positive-orientation--->-25-->
> > 
> > 
> > 
> > The last question is about the umbrella sampling.
> > I learnt from [gmx-users] Re: doubt about your Umbrella Sampling tutorial 
> > that it's ok to remove the pores of Chain B during the US. But in longer 
> > simulation time and in the periodical box, will the COM of Chain B and A be 
> > affacted by the boundary? and then affact the calculation of US potential?
> > 
> 
> The tutorial system won't work if you turn off the restraint.  Eventually the 
> system will rotate and the groups will cross periodic boundaries, which will 
> cause the chosen pull geometry to fail.  So the restraints serve a dual 
> purpose: 
> (1) to mimic the stability of larger amyloid assemblies and (2) to reduce the 
> system size, as several hundred thousand atoms was not feasible for me at the 
> time.


So your point is that during US, we can't remove the Chain B's restrain. Right?
During US, is there any means to study the flexiblity of both groups? (i.e. 
there is no restrain on both groups except the umbrella potential between them 
and at the same time both groups will not cross periodic boundaries and will 
not affact the umbrella potential geometry, which is a necessary part of my 
study)

Yu


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[gmx-users] Periodic Molecule's Free Energy Calculation Error

[Jason Zhu]

Hello Gromacs Community,

I am trying to calculate the solvation free energy of a hBN sheet following
Justin Lemkul and Alchemistry's tutorials.
Since the hBN sheet is infinitely large, I turned the periodic molecules
flag on.
This runs all fine on one core, but when I try to run NVT in parallel (e.g.
4 ranks), the job would throw the following error:

A list of missing interactions:
LJC Pairs NB of 890400 missing 338688

---
Program gmx mdrun, VERSION 5.1.4
Source code file:
/gpfs/runtime/opt/gromacs/5.1.4/src/gromacs-5.1.4/src/gromacs/domdec/domdec_topology.cpp,
line: 242

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

Halting parallel program gmx mdrun on rank 1 out of 4
In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process
1)

---
Program gmx mdrun, VERSION 5.1.4
Source code file:
/gpfs/runtime/opt/gromacs/5.1.4/src/gromacs-5.1.4/src/gromacs/domdec/domdec_topology.cpp,
line: 242

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

It seems like a domain decomposition error. My first thought was that the
system "explode".
However, when I check my topology and pbc condition carefully, there is no
sign of anything wrong.
I also tried NPT & PROD MD. The same error when I ran on multiple MPI
threads.

My question is: why the system could run fine on one MPI, but not if I
increased the number of MPI threads?

Any help on this issue will be really appreciated.


Here below is my .mdp file:

; RUN CONTROL—NVT
;——
define   = -DPOSRES_HBN
integrator   = sd; stochastic leap-frog integrator
nsteps   = 5000  ; 2 * 5,000 fs = 10 ps
dt   = 0.002 ; 2 fs
comm-mode= Linear; remove center of mass translation
nstcomm  = 100   ; frequency for center of mass motion removal

;——
; OUTPUT CONTROL
;——
nstxout= 0  ; don't save coordinates to .trr
nstvout= 0  ; don't save velocities to .trr
nstfout= 0  ; don't save forces to .trr
nstxout-compressed = 5000   ; xtc compressed trajectory output
every 5000 steps
compressed-x-precision = 1000   ; precision with which to write to the
compressed trajectory file
nstlog = 5000   ; update log file every 10 ps
nstenergy  = 5000   ; save energies every 10 ps
nstcalcenergy  = 100; calculate energies every 100 steps

;——
; BONDS
;——
constraint_algorithm   = lincs  ; holonomic constraints
constraints= all-bonds  ; hydrogens only are constrained
lincs_iter = 1  ; accuracy of LINCS (1 is default)
lincs_order= 4  ; also related to accuracy (4 is
default)
lincs-warnangle= 30 ; maximum angle that a bond can rotate
before LINCS will complain (30 is default)
continuation   = no ; formerly known as
'unconstrained-start' - useful for exact continuations and reruns

;——
; NEIGHBOR SEARCHING
;——
cutoff-scheme   = Verlet
ns-type = grid   ; search neighboring grid cells
nstlist = 10 ; 20 fs (default is 10)
rlist   = 1.2; short-range neighborlist cutoff (in nm)
pbc = xyz; 3D PBC
; PBC: grp is infinite
periodic-molecules = yes

;——
; ELECTROSTATICS
;——
coulombtype  = PME  ; Particle Mesh Ewald for long-range
electrostatics
rcoulomb = 1.2  ; short-range electrostatic cutoff (in nm)
ewald_geometry   = 3d   ; Ewald sum is performed in all three dimensions
pme-order= 4; interpolation order for PME (default is 4)
fourierspacing   = 0.16 ; grid spacing for FFT
ewald-rtol   = 1e-6 ; relative strength of the Ewald-shifted direct
potential at rcoulomb

;——
; VDW
;——
vdw-type= PME
rvdw= 1.2
vdw-modifier= Potential-Shift
ewald-rtol-lj   = 1e-3
lj-pme-comb-rule= Geometric
DispCorr= EnerPres

;——
; TEMPERATURE & PRESSURE COUPL
;——
tc_grps=  System
tau_t  =  0.1
ref_t  =  300
pcoupl =  no

;——
; VELOCITY GENERATION
;——
gen_ve

Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

[Alex]

hBN is hardly a common subject of simulation for Gromacs folks, but 
let's see...


1. When you run the simulation in vacuum, do you get the same error? 
Does a 300K vacuum simulation result in reasonable sheet behavior? What 
about NVT?


2. What GROMACS forcefield are you using and what are the nonbonded 
types for boron and nitrogen?


3. How was the topology obtained? If x2top was used, was the BN sample 
in a box with in-plane PBC?


Alex


On 7/11/2017 8:39 PM, Jason Zhu wrote:

Hello Gromacs Community,

I am trying to calculate the solvation free energy of a hBN sheet following
Justin Lemkul and Alchemistry's tutorials.
Since the hBN sheet is infinitely large, I turned the periodic molecules
flag on.
This runs all fine on one core, but when I try to run NVT in parallel (e.g.
4 ranks), the job would throw the following error:

A list of missing interactions:
 LJC Pairs NB of 890400 missing 338688

---
Program gmx mdrun, VERSION 5.1.4
Source code file:
/gpfs/runtime/opt/gromacs/5.1.4/src/gromacs-5.1.4/src/gromacs/domdec/domdec_topology.cpp,
line: 242

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

Halting parallel program gmx mdrun on rank 1 out of 4
In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process
1)

---
Program gmx mdrun, VERSION 5.1.4
Source code file:
/gpfs/runtime/opt/gromacs/5.1.4/src/gromacs-5.1.4/src/gromacs/domdec/domdec_topology.cpp,
line: 242

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

It seems like a domain decomposition error. My first thought was that the
system "explode".
However, when I check my topology and pbc condition carefully, there is no
sign of anything wrong.
I also tried NPT & PROD MD. The same error when I ran on multiple MPI
threads.

My question is: why the system could run fine on one MPI, but not if I
increased the number of MPI threads?

Any help on this issue will be really appreciated.


Here below is my .mdp file:

; RUN CONTROL—NVT
;——
define   = -DPOSRES_HBN
integrator   = sd; stochastic leap-frog integrator
nsteps   = 5000  ; 2 * 5,000 fs = 10 ps
dt   = 0.002 ; 2 fs
comm-mode= Linear; remove center of mass translation
nstcomm  = 100   ; frequency for center of mass motion removal

;——
; OUTPUT CONTROL
;——
nstxout= 0  ; don't save coordinates to .trr
nstvout= 0  ; don't save velocities to .trr
nstfout= 0  ; don't save forces to .trr
nstxout-compressed = 5000   ; xtc compressed trajectory output
every 5000 steps
compressed-x-precision = 1000   ; precision with which to write to the
compressed trajectory file
nstlog = 5000   ; update log file every 10 ps
nstenergy  = 5000   ; save energies every 10 ps
nstcalcenergy  = 100; calculate energies every 100 steps

;——
; BONDS
;——
constraint_algorithm   = lincs  ; holonomic constraints
constraints= all-bonds  ; hydrogens only are constrained
lincs_iter = 1  ; accuracy of LINCS (1 is default)
lincs_order= 4  ; also related to accuracy (4 is
default)
lincs-warnangle= 30 ; maximum angle that a bond can rotate
before LINCS will complain (30 is default)
continuation   = no ; formerly known as
'unconstrained-start' - useful for exact continuations and reruns

;——
; NEIGHBOR SEARCHING
;——
cutoff-scheme   = Verlet
ns-type = grid   ; search neighboring grid cells
nstlist = 10 ; 20 fs (default is 10)
rlist   = 1.2; short-range neighborlist cutoff (in nm)
pbc = xyz; 3D PBC
; PBC: grp is infinite
periodic-molecules = yes

;——
; ELECTROSTATICS
;——
coulombtype  = PME  ; Particle Mesh Ewald for long-range
electrostatics
rcoulomb = 1.2  ; short-range electrostatic cutoff (in nm)
ewald_geometry   = 3d   ; Ewald sum is performed in all three dimensions
pme-order= 4; interpolation order for PME (default is 4)
fourierspacing   = 0.16 ; grid spacing for FFT
ewald-rtol   = 1e-6 ; relative strength of the Ewald-shifted direct
potential at rcoulomb

;—

[gmx-users] Accessible Surface Area (ASA) for each residue per frame

[Maximilian Ebert]

Hi there,
Is there a way using gmx sasa or gmx do_dssp to get the ASA per residue per 
frame? I only find option to extract the average over all frames per residue.
Thanks,
Max
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[gmx-users] RDF

[Vidya R]

Hi,

I want to calculate RDF of my organic molecule with a solvent.

What should be the duration of my simulation?

Is 100 ps enough?


Thanks,
Vidya.R
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Re: [gmx-users] Modifying force field for graphene

[‪Mohammad Roostaie‬ ‪]

Thank you very much Alex.
Mohammad

  From: Alex 
 To: gmx-us...@gromacs.org; ‪Mohammad Roostaie‬ ‪  
 Sent: Tuesday, 11 July 2017, 22:54:56
 Subject: Re: [gmx-users] Modifying force field for graphene
   
The answer is yes, OPLSAA does need to be slightly edited for graphene 
and nanotubes to work, assuming you find good parameters for graphene. 
Google is strong with you, use it.

Alex

On 7/11/2017 8:34 AM, ‪Mohammad Roostaie‬ ‪ wrote:
> Hi All,
> I want to simulate graphene by using OPLS_AA force field. Does this force 
> field need any modification for graphene simulation?If yes, do you have any 
> link tutorial for the modification?
> Kind regards,Mohammad



   
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[gmx-users] Add missing residues

[Khadija Amine]

Hello everyone,
Can someone post the best tool available for building missing residues in
the crystal structure?
I need the complete structure (2 missing residues) for carrying out
simulation studies.
 Thank you

*Khadija Amine*
Ph.D. Biology and Health
Biochemistry & Bioinformatics
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