[gmx-users] Simulation on multi nodes performance

[Ali Ahmed]

Hello GMX users

I'm trying to do simulations on multi nodes so I used  8 nodes (128
processors). AS I see there is no difference between 1 node and 8 nodes.

I used these commands:

---

load apps/gromacs-2016

load apps/openmpi-2.1.1

gmx grompp -f EMZ.mdp -c BOX.gro -p TOP.top -o EMZ.tpr

mpirun -np 128 mdrun_mpi -v -deffnm EMZ



I'm kind of confused about the right commands

Any comment will be helpful

Thanks in advance

Ali
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Re: [gmx-users] pH dependent simulation

[Tasneem Kausar]

pKa of amino acid residue is a constant quantity. Depending on the pH you
can protonate and deprotonate amino acid according to the pKa of particular
residue.


Virus-free.
www.avast.com

<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

On Mon, Nov 27, 2017 at 9:39 AM,  wrote:

> Hello Everyone
>
> I am trying to simulate a protein at two pH (7.4 and 9.0) using
> gromacs 5.1.4. The protein has no missing residues. Optimal pH range is
> 6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17
> positively charged residues.
>
> However upon predicting the pKa values using H++ server, I am getting the
> same pKa values for all the charged residues (at pH 7.4 and pH 9). And the
> total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it
> should have different pKa values at pH 7 and 9).
>
> Whether I am in the right direction or doing something wrong!!!
>
> Can anyone kindly suggest me how to proceed further?
>
> Any suggestion is appreciated.
>
> Thank You
> Zaved
>
>
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[gmx-users] pH dependent simulation

[zaved]

Hello Everyone

I am trying to simulate a protein at two pH (7.4 and 9.0) using
gromacs 5.1.4. The protein has no missing residues. Optimal pH range is
6.0 to 9.0 and pI of the protein is 11.4. It has 9 negatively and 17
positively charged residues.

However upon predicting the pKa values using H++ server, I am getting the
same pKa values for all the charged residues (at pH 7.4 and pH 9). And the
total charge of +8e is also same at both pH 7.4 and 9.0. (Instead it
should have different pKa values at pH 7 and 9).

Whether I am in the right direction or doing something wrong!!!

Can anyone kindly suggest me how to proceed further?

Any suggestion is appreciated.

Thank You
Zaved


* * * D I S C L A I M E R * * *
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individual named. If you are not the named addressee you should not 
disseminate, distribute or copy this e-mail. Please notify the sender 
immediately by e-mail if you have received this e-mail in error and destroy it 
from your system. Though considerable effort has been made to deliver error 
free e-mail messages but it can not be guaranteed to be secure or error-free as 
information could be intercepted, corrupted, lost, destroyed, delayed, or may 
contain viruses. The recipient must verify the integrity of this e-mail message.
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Re: [gmx-users] cmap

[Justin Lemkul]

On 11/26/17 6:33 PM, MD wrote:

Hi Justin,
I added the CSO to residuetypes.dat in my local computer and it worked now.
I then tried to copy the modified "residuetypes.dat" to the ff  folder on
the server computer, but the server computer gromacs wouldn't give option
to choose which residuetypes.dat to use. Do you know how to let it choose
instead of using its original one by default?


Keep it in the working directory when running pdb2gmx. All GROMACS 
programs search the working directory first before looking in $GMXLIB.


-Justin


Thanks,
Ming

On Sun, Nov 26, 2017 at 6:11 PM, Justin Lemkul  wrote:



On 11/26/17 6:06 PM, MD wrote:


Hi,

I had to repost this cause of the size of the previous thread.

I had another error after grompp, "ERROR 1 [file
topol_Protein_chain_E.itp,
line 52165]:
Unknown cmap torsion between atoms 3022 3024 3026 3046 3049"

The 3022 3024 3026 3046 3049 in the itp files referred to the backbone
(C-N-CA-C-N) of three connected residues R-W-T..

I found out it is the W that causing issue. I am not sure why it has one
CC, two OT1 instead of one  C and O like the rest of the Trp residues in
the protein. This is the only Trp that has these parameters.
   Any suggestions?


This is the C-terminal Trp residue, hence the carbonyl becomes a
carboxylate.  There should not be a CMAP generated for a C-terminal residue
and pdb2gmx should have removed that interaction.

If this is the residue preceding CSO, then you are getting a false chain
termination because you haven't added CSO to residuetypes.dat.

-Justin


residue 196 TRP rtp TRP  q -1.0

3024NH1196TRP  N   3024  -0.47 14.007   ;
qtot 8.53
3025  H196TRP HN   3025   0.31  1.008   ;
qtot 8.84
3026CT1196TRP CA   3026   0.07 12.011   ;
qtot 8.91
3027HB1196TRP HA   3027   0.09  1.008   ;
qtot 9
3028CT2196TRP CB   3028  -0.18 12.011   ;
qtot 8.82
3029HA2196TRPHB1   3029   0.09  1.008   ;
qtot 8.91
3030HA2196TRPHB2   3030   0.09  1.008   ;
qtot 9
3031 CY196TRP CG   3031  -0.03 12.011   ;
qtot 8.97
3032 CA196TRPCD1   3032  -0.15 12.011   ;
qtot 8.82
3033 HP196TRPHD1   3033   0.22  1.008   ;
qtot 9.04
3034 NY196TRPNE1   3034  -0.51 14.007   ;
qtot 8.53
3035  H196TRPHE1   3035   0.37  1.008   ;
qtot 8.9
3036CPT196TRPCE2   3036   0.24 12.011   ;
qtot 9.14
3037CPT196TRPCD2   3037   0.11 12.011   ;
qtot 9.25
3038CAI196TRPCE3   3038  -0.25 12.011   ;
qtot 9
3039 HP196TRPHE3   3039   0.17  1.008   ;
qtot 9.17
3040 CA196TRPCZ3   3040   -0.2 12.011   ;
qtot 8.97
3041 HP196TRPHZ3   3041   0.14  1.008   ;
qtot 9.11
3042CAI196TRPCZ2   3042  -0.27 12.011   ;
qtot 8.84
3043 HP196TRPHZ2   3043   0.16  1.008   ;
qtot 9
3044 CA196TRPCH2   3044  -0.14 12.011   ;
qtot 8.86
3045 HP196TRPHH2   3045   0.14  1.008   ;
qtot 9
3046 CC196TRP  C   3046   0.34 12.011   ;
qtot 9.34
3047 OC196TRPOT1   3047  -0.6715.9994   ;
qtot 8.67
3048 OC196TRPOT2   3048  -0.6715.9994   ;
qtot 8


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] cmap

[MD]

Hi Justin,
I added the CSO to residuetypes.dat in my local computer and it worked now.
I then tried to copy the modified "residuetypes.dat" to the ff  folder on
the server computer, but the server computer gromacs wouldn't give option
to choose which residuetypes.dat to use. Do you know how to let it choose
instead of using its original one by default?
Thanks,
Ming

On Sun, Nov 26, 2017 at 6:11 PM, Justin Lemkul  wrote:

>
>
> On 11/26/17 6:06 PM, MD wrote:
>
>> Hi,
>>
>> I had to repost this cause of the size of the previous thread.
>>
>> I had another error after grompp, "ERROR 1 [file
>> topol_Protein_chain_E.itp,
>> line 52165]:
>>Unknown cmap torsion between atoms 3022 3024 3026 3046 3049"
>>
>> The 3022 3024 3026 3046 3049 in the itp files referred to the backbone
>> (C-N-CA-C-N) of three connected residues R-W-T..
>>
>> I found out it is the W that causing issue. I am not sure why it has one
>> CC, two OT1 instead of one  C and O like the rest of the Trp residues in
>> the protein. This is the only Trp that has these parameters.
>>   Any suggestions?
>>
>
> This is the C-terminal Trp residue, hence the carbonyl becomes a
> carboxylate.  There should not be a CMAP generated for a C-terminal residue
> and pdb2gmx should have removed that interaction.
>
> If this is the residue preceding CSO, then you are getting a false chain
> termination because you haven't added CSO to residuetypes.dat.
>
> -Justin
>
>
> residue 196 TRP rtp TRP  q -1.0
>>3024NH1196TRP  N   3024  -0.47 14.007   ;
>> qtot 8.53
>>3025  H196TRP HN   3025   0.31  1.008   ;
>> qtot 8.84
>>3026CT1196TRP CA   3026   0.07 12.011   ;
>> qtot 8.91
>>3027HB1196TRP HA   3027   0.09  1.008   ;
>> qtot 9
>>3028CT2196TRP CB   3028  -0.18 12.011   ;
>> qtot 8.82
>>3029HA2196TRPHB1   3029   0.09  1.008   ;
>> qtot 8.91
>>3030HA2196TRPHB2   3030   0.09  1.008   ;
>> qtot 9
>>3031 CY196TRP CG   3031  -0.03 12.011   ;
>> qtot 8.97
>>3032 CA196TRPCD1   3032  -0.15 12.011   ;
>> qtot 8.82
>>3033 HP196TRPHD1   3033   0.22  1.008   ;
>> qtot 9.04
>>3034 NY196TRPNE1   3034  -0.51 14.007   ;
>> qtot 8.53
>>3035  H196TRPHE1   3035   0.37  1.008   ;
>> qtot 8.9
>>3036CPT196TRPCE2   3036   0.24 12.011   ;
>> qtot 9.14
>>3037CPT196TRPCD2   3037   0.11 12.011   ;
>> qtot 9.25
>>3038CAI196TRPCE3   3038  -0.25 12.011   ;
>> qtot 9
>>3039 HP196TRPHE3   3039   0.17  1.008   ;
>> qtot 9.17
>>3040 CA196TRPCZ3   3040   -0.2 12.011   ;
>> qtot 8.97
>>3041 HP196TRPHZ3   3041   0.14  1.008   ;
>> qtot 9.11
>>3042CAI196TRPCZ2   3042  -0.27 12.011   ;
>> qtot 8.84
>>3043 HP196TRPHZ2   3043   0.16  1.008   ;
>> qtot 9
>>3044 CA196TRPCH2   3044  -0.14 12.011   ;
>> qtot 8.86
>>3045 HP196TRPHH2   3045   0.14  1.008   ;
>> qtot 9
>>3046 CC196TRP  C   3046   0.34 12.011   ;
>> qtot 9.34
>>3047 OC196TRPOT1   3047  -0.6715.9994   ;
>> qtot 8.67
>>3048 OC196TRPOT2   3048  -0.6715.9994   ;
>> qtot 8
>>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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Re: [gmx-users] .cpt file

[Justin Lemkul]

On 11/26/17 6:20 PM, rose rahmani wrote:

Hi;

Why .cpt files are not as much important as other files (since grompp works
without it)?


Can you please provide some context for this question?

I'd call a checkpoint file essential, as it is the only true way to get 
an exact continuation of a stopped run, and also eliminates the need to 
invoke grompp at all in the vast majority of all continuations.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] .cpt file

[rose rahmani]

Hi;

Why .cpt files are not as much important as other files (since grompp works
without it)?
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Re: [gmx-users] cmap

[Justin Lemkul]

On 11/26/17 6:06 PM, MD wrote:

Hi,

I had to repost this cause of the size of the previous thread.

I had another error after grompp, "ERROR 1 [file topol_Protein_chain_E.itp,
line 52165]:
   Unknown cmap torsion between atoms 3022 3024 3026 3046 3049"

The 3022 3024 3026 3046 3049 in the itp files referred to the backbone
(C-N-CA-C-N) of three connected residues R-W-T..

I found out it is the W that causing issue. I am not sure why it has one
CC, two OT1 instead of one  C and O like the rest of the Trp residues in
the protein. This is the only Trp that has these parameters.
  Any suggestions?


This is the C-terminal Trp residue, hence the carbonyl becomes a 
carboxylate.  There should not be a CMAP generated for a C-terminal 
residue and pdb2gmx should have removed that interaction.


If this is the residue preceding CSO, then you are getting a false chain 
termination because you haven't added CSO to residuetypes.dat.


-Justin


residue 196 TRP rtp TRP  q -1.0
   3024NH1196TRP  N   3024  -0.47 14.007   ;
qtot 8.53
   3025  H196TRP HN   3025   0.31  1.008   ;
qtot 8.84
   3026CT1196TRP CA   3026   0.07 12.011   ;
qtot 8.91
   3027HB1196TRP HA   3027   0.09  1.008   ;
qtot 9
   3028CT2196TRP CB   3028  -0.18 12.011   ;
qtot 8.82
   3029HA2196TRPHB1   3029   0.09  1.008   ;
qtot 8.91
   3030HA2196TRPHB2   3030   0.09  1.008   ;
qtot 9
   3031 CY196TRP CG   3031  -0.03 12.011   ;
qtot 8.97
   3032 CA196TRPCD1   3032  -0.15 12.011   ;
qtot 8.82
   3033 HP196TRPHD1   3033   0.22  1.008   ;
qtot 9.04
   3034 NY196TRPNE1   3034  -0.51 14.007   ;
qtot 8.53
   3035  H196TRPHE1   3035   0.37  1.008   ;
qtot 8.9
   3036CPT196TRPCE2   3036   0.24 12.011   ;
qtot 9.14
   3037CPT196TRPCD2   3037   0.11 12.011   ;
qtot 9.25
   3038CAI196TRPCE3   3038  -0.25 12.011   ;
qtot 9
   3039 HP196TRPHE3   3039   0.17  1.008   ;
qtot 9.17
   3040 CA196TRPCZ3   3040   -0.2 12.011   ;
qtot 8.97
   3041 HP196TRPHZ3   3041   0.14  1.008   ;
qtot 9.11
   3042CAI196TRPCZ2   3042  -0.27 12.011   ;
qtot 8.84
   3043 HP196TRPHZ2   3043   0.16  1.008   ;
qtot 9
   3044 CA196TRPCH2   3044  -0.14 12.011   ;
qtot 8.86
   3045 HP196TRPHH2   3045   0.14  1.008   ;
qtot 9
   3046 CC196TRP  C   3046   0.34 12.011   ;
qtot 9.34
   3047 OC196TRPOT1   3047  -0.6715.9994   ;
qtot 8.67
   3048 OC196TRPOT2   3048  -0.6715.9994   ;
qtot 8


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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[gmx-users] cmap

[MD]

Hi,

I had to repost this cause of the size of the previous thread.

I had another error after grompp, "ERROR 1 [file topol_Protein_chain_E.itp,
line 52165]:
  Unknown cmap torsion between atoms 3022 3024 3026 3046 3049"

The 3022 3024 3026 3046 3049 in the itp files referred to the backbone
(C-N-CA-C-N) of three connected residues R-W-T..

I found out it is the W that causing issue. I am not sure why it has one
CC, two OT1 instead of one  C and O like the rest of the Trp residues in
the protein. This is the only Trp that has these parameters.
 Any suggestions?

residue 196 TRP rtp TRP  q -1.0
  3024NH1196TRP  N   3024  -0.47 14.007   ;
qtot 8.53
  3025  H196TRP HN   3025   0.31  1.008   ;
qtot 8.84
  3026CT1196TRP CA   3026   0.07 12.011   ;
qtot 8.91
  3027HB1196TRP HA   3027   0.09  1.008   ;
qtot 9
  3028CT2196TRP CB   3028  -0.18 12.011   ;
qtot 8.82
  3029HA2196TRPHB1   3029   0.09  1.008   ;
qtot 8.91
  3030HA2196TRPHB2   3030   0.09  1.008   ;
qtot 9
  3031 CY196TRP CG   3031  -0.03 12.011   ;
qtot 8.97
  3032 CA196TRPCD1   3032  -0.15 12.011   ;
qtot 8.82
  3033 HP196TRPHD1   3033   0.22  1.008   ;
qtot 9.04
  3034 NY196TRPNE1   3034  -0.51 14.007   ;
qtot 8.53
  3035  H196TRPHE1   3035   0.37  1.008   ;
qtot 8.9
  3036CPT196TRPCE2   3036   0.24 12.011   ;
qtot 9.14
  3037CPT196TRPCD2   3037   0.11 12.011   ;
qtot 9.25
  3038CAI196TRPCE3   3038  -0.25 12.011   ;
qtot 9
  3039 HP196TRPHE3   3039   0.17  1.008   ;
qtot 9.17
  3040 CA196TRPCZ3   3040   -0.2 12.011   ;
qtot 8.97
  3041 HP196TRPHZ3   3041   0.14  1.008   ;
qtot 9.11
  3042CAI196TRPCZ2   3042  -0.27 12.011   ;
qtot 8.84
  3043 HP196TRPHZ2   3043   0.16  1.008   ;
qtot 9
  3044 CA196TRPCH2   3044  -0.14 12.011   ;
qtot 8.86
  3045 HP196TRPHH2   3045   0.14  1.008   ;
qtot 9
  3046 CC196TRP  C   3046   0.34 12.011   ;
qtot 9.34
  3047 OC196TRPOT1   3047  -0.6715.9994   ;
qtot 8.67
  3048 OC196TRPOT2   3048  -0.6715.9994   ;
qtot 8
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Re: [gmx-users] umbrella sampling

[rose rahmani]

On Mon, Nov 27, 2017 at 1:55 AM, Alex  wrote:

> Hi,
>
> The answer is clearly in the error, just read it please:
> 2.848793 > 0.49 * (4/2) where 4 is the box length.
>
> You can either keep the “pull_coord1_geometry= distance” and increase
> the box length or change the “pull_coord1_geometry” to  “=
> direction-periodic“. I prefer the former though.
>
> Cheers,
> Alex
>
>> I've got it.
>
> would you please answer to another questions too? thank you in advance
>
>

>
>
> On Sun, Nov 26, 2017 at 23:10 rose rahmani  wrote:
>
> > Hi;
> >
> > This is md_pull.mdp
> >
> > integrator   = md
> > dt   = 0.001
> > nsteps   = 200
> > nstxout  = 0
> > nstvout  = 0
> > nstfout  = 0
> > nstlog   = 500
> > nstenergy= 1000
> > nstxtcout= 1000
> > rlist= 1.5
> > rcoulomb = 1.5
> > rvdw = 1.2
> > coulombtype  = pme
> > cutoff-scheme= group
> > vdwtype  = Switch
> > rvdw_switch  = 1.0
> > pcoupl   = no
> > gen-vel  = yes
> > gen-temp = 0
> > gen-seed = 173529
> > constraints  = h-bonds
> > pbc  = xy
> > freezegrps   = WAL ZnS
> > freezedim= Y Y Y Y Y Y
> > energygrp-excl   = WAL WAL ZnS ZnS
> > energygrps   = SOL WAL ZnS Protein NA CL
> > nwall= 2
> > wall-atomtype= C C
> > wall-type= 9-3
> > wall-density = 150 150
> > wall-ewald-zfac  = 3
> > ewald-geometry   = 3dc
> > fourierspacing   = 0.12
> > tcoupl   = v-rescale
> > tc-grps  = System
> > tau-t= 0.1
> > ref-t= 300
> > pull= yes
> > pull_ngroups= 2
> > pull_ncoords= 1
> > pull_group1_name= ZnS
> > pull_group2_name= Protein
> > pull_coord1_type= umbrella
> > pull_coord1_geometry= distance
> > pull_coord1_groups  = 1 2
> > pull__coord1_dim= N N Y
> > pull_coord1_rate  = -0.001; 1 nm per  ns
> > pull_coord1_k = 5000
> > pull_coord1_start  = yes
> >
> > Program gmx grompp, VERSION 5.1.4
> >
> > Fatal error:
> > Distance between pull groups 1 and 2 (2.848793 nm) is larger than 0.49
> > times the box size (2.00).
> > You might want to consider using "pull-geometry = direction-periodic"
> > instead.
> >
> > the box size is= 4 4 12
> >
> > could you please help me to resolve it?
> > -
> > Mr.Lemkul told me rcutt-off is wrong and
> >
> >  i should'nt put "cutoff-scheme= group" >>>but when i remove
> > it i'll get  this error too;
> >
> >   >>With Verlet lists rcoulomb!=rvdw is not supported
> >
> > i know it's wrong solution but what is my alternative?!!
> >
> > --
> > -dummy particle should move towards the surface with a constant speed of
> 1
> > nm/ns from z = 2 nm to z = 0 and drags the CM by the harmonic force
> > corresponding to the spring constant of 5000.
> >
> > I DON'T know how should i implement deltaZ(=2)? which .mdp option refers
> to
> > it?!
> >
> > thank you so much
> >
> > Best regards
> > Rose
> > --
> > 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.
> >
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Re: [gmx-users] umbrella sampling

[Alex]

Hi,

The answer is clearly in the error, just read it please:
2.848793 > 0.49 * (4/2) where 4 is the box length.

You can either keep the “pull_coord1_geometry= distance” and increase
the box length or change the “pull_coord1_geometry” to  “=
direction-periodic“. I prefer the former though.

Cheers,
Alex

On Sun, Nov 26, 2017 at 23:10 rose rahmani  wrote:

> Hi;
>
> This is md_pull.mdp
>
> integrator   = md
> dt   = 0.001
> nsteps   = 200
> nstxout  = 0
> nstvout  = 0
> nstfout  = 0
> nstlog   = 500
> nstenergy= 1000
> nstxtcout= 1000
> rlist= 1.5
> rcoulomb = 1.5
> rvdw = 1.2
> coulombtype  = pme
> cutoff-scheme= group
> vdwtype  = Switch
> rvdw_switch  = 1.0
> pcoupl   = no
> gen-vel  = yes
> gen-temp = 0
> gen-seed = 173529
> constraints  = h-bonds
> pbc  = xy
> freezegrps   = WAL ZnS
> freezedim= Y Y Y Y Y Y
> energygrp-excl   = WAL WAL ZnS ZnS
> energygrps   = SOL WAL ZnS Protein NA CL
> nwall= 2
> wall-atomtype= C C
> wall-type= 9-3
> wall-density = 150 150
> wall-ewald-zfac  = 3
> ewald-geometry   = 3dc
> fourierspacing   = 0.12
> tcoupl   = v-rescale
> tc-grps  = System
> tau-t= 0.1
> ref-t= 300
> pull= yes
> pull_ngroups= 2
> pull_ncoords= 1
> pull_group1_name= ZnS
> pull_group2_name= Protein
> pull_coord1_type= umbrella
> pull_coord1_geometry= distance
> pull_coord1_groups  = 1 2
> pull__coord1_dim= N N Y
> pull_coord1_rate  = -0.001; 1 nm per  ns
> pull_coord1_k = 5000
> pull_coord1_start  = yes
>
> Program gmx grompp, VERSION 5.1.4
>
> Fatal error:
> Distance between pull groups 1 and 2 (2.848793 nm) is larger than 0.49
> times the box size (2.00).
> You might want to consider using "pull-geometry = direction-periodic"
> instead.
>
> the box size is= 4 4 12
>
> could you please help me to resolve it?
> -
> Mr.Lemkul told me rcutt-off is wrong and
>
>  i should'nt put "cutoff-scheme= group" >>>but when i remove
> it i'll get  this error too;
>
>   >>With Verlet lists rcoulomb!=rvdw is not supported
>
> i know it's wrong solution but what is my alternative?!!
>
> --
> -dummy particle should move towards the surface with a constant speed of 1
> nm/ns from z = 2 nm to z = 0 and drags the CM by the harmonic force
> corresponding to the spring constant of 5000.
>
> I DON'T know how should i implement deltaZ(=2)? which .mdp option refers to
> it?!
>
> thank you so much
>
> Best regards
> Rose
> --
> 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.
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[gmx-users] umbrella sampling

[rose rahmani]

Hi;

This is md_pull.mdp

integrator   = md
dt   = 0.001
nsteps   = 200
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
rlist= 1.5
rcoulomb = 1.5
rvdw = 1.2
coulombtype  = pme
cutoff-scheme= group
vdwtype  = Switch
rvdw_switch  = 1.0
pcoupl   = no
gen-vel  = yes
gen-temp = 0
gen-seed = 173529
constraints  = h-bonds
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnS ZnS
energygrps   = SOL WAL ZnS Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= ZnS
pull_group2_name= Protein
pull_coord1_type= umbrella
pull_coord1_geometry= distance
pull_coord1_groups  = 1 2
pull__coord1_dim= N N Y
pull_coord1_rate  = -0.001; 1 nm per  ns
pull_coord1_k = 5000
pull_coord1_start  = yes

Program gmx grompp, VERSION 5.1.4

Fatal error:
Distance between pull groups 1 and 2 (2.848793 nm) is larger than 0.49
times the box size (2.00).
You might want to consider using "pull-geometry = direction-periodic"
instead.

the box size is= 4 4 12

could you please help me to resolve it?
-
Mr.Lemkul told me rcutt-off is wrong and

 i should'nt put "cutoff-scheme= group" >>>but when i remove
it i'll get  this error too;

  >>With Verlet lists rcoulomb!=rvdw is not supported

i know it's wrong solution but what is my alternative?!!

--
-dummy particle should move towards the surface with a constant speed of 1
nm/ns from z = 2 nm to z = 0 and drags the CM by the harmonic force
corresponding to the spring constant of 5000.

I DON'T know how should i implement deltaZ(=2)? which .mdp option refers to
it?!

thank you so much

Best regards
Rose
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Re: [gmx-users] Build thin film.

[Dallas Warren]

You can do whatever you want, and there are many tools to help you do that.

Couple of options are using gmx insert-molecules (constrain the box
size to make the film, then enlarge afterwards to insert other
molecules), gmx genconf (just stack as required, some initial care
with runs will be required to get to correct size/density), or packmol
(http://www.ime.unicamp.br/~martinez/packmol/home.shtml)
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 24 November 2017 at 03:51, ali akgün  wrote:
> I have a pdb file can i build thin film  ?
> --
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Re: [gmx-users] gmx angle memory consumption

[Dallas Warren]

 Matthias,

GROMACS only writes to a file when the amount of data reaches a
certain threshold, prior to that it is just stored in memory.  I don't
know what that chunk size is.

It may be the manner in which the analysis script stores the
trajectory data in memory?  Hopefully a developer will be able to
provide some insight.  Recommend you do some exploration on what
triggers this, to provide them with further information.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 21 November 2017 at 23:30, Matthias Ernst
 wrote:
> Hi,
>
> I want to calculate dihedral angles for long trajectories at high
> sampling rates using gmx angle as follows:
>
> gmx angle -f traj.xtc -n dih_indices.ndx -ov dih.xvg -type dihedral -all
>
> After some time, it completely fills my RAM without having written
> anything to the output file.  As the system starts swapping, everything
> becomes incredibly slow.
> I thought gmx tools usually process trajectories frame-wise and output
> immediately (or in some chunks), but this seems not to be the case here.
> Could it be gmx angle is storing the values in RAM and only writes them
> out at the end of the analysis?
>
> Thanks a lot,
> Matthias
>
>
> --
> http://phdcomics.com/comics/archive.php?comicid=1936
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Re: [gmx-users] virtual site connected to dummy massive site

[Mark Abraham]

Hi,

Your linear version has two rotation axes (and thus DOF) because it has
mass distribution. Your point version has no mass distribution.

Mark

On Sun, Nov 26, 2017 at 7:52 PM Faezeh Pousaneh  wrote:

> Please note that the carbon is a virtual site, so has not mass. So the DOF
> does not influence of its configurations on average. Besides the angle   of
> M--C--M is always 180.
>
> Mark, I compare the results of average distributions not a snapshot.
>
> Justin, the only LJ are from atom C with next molecules in both systems.
> (In fact I got the idea from your carbon dioxide tutorial, in which later I
> will add two more virtual sites with charges to create a dipole moment for
> my atom (e.g C here), but first I must understand this stage)
>
>
>
> Best regards
>
>
> On Sun, Nov 26, 2017 at 7:12 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > On Sun, Nov 26, 2017 at 6:35 PM Faezeh Pousaneh 
> > wrote:
> >
> > > Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand
> > my
> > > question, I have no charges in systems on any atoms. So the extra DOF
> do
> > > not effect on potential.
> > >
> >
> > Charge has nothing to do with it. The potential is computed from all the
> > interactions in the system, which in your case includes LJ. You aren't
> > going to generate the same ensemble of configurations in your two cases,
> so
> > you cannot expect to observe the same distribution of potential energy.
> >
> > Note that it would have been nice to say whether you were comparing a
> > distribution of energies or a snapshot. As it is, we are guessing.
> >
> > Mark
> >
> > Best regards
> > >
> > >
> > > On Fri, Nov 24, 2017 at 11:03 AM, Mark Abraham <
> mark.j.abra...@gmail.com
> > >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > Potential energy is a function of configuration. You can expect the
> > same
> > > LJ
> > > > energy if you compare the same configuration, ie that the
> distribution
> > of
> > > > states is identical. But if you would have the same total energy and
> a
> > > > different distribution between PE and KE (because the DOF change)
> then
> > > you
> > > > will not sample the same states.
> > > >
> > > > Mark
> > > >
> > > > On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh <
> fpoosa...@gmail.com>
> > > > wrote:
> > > >
> > > > > Dear Mark,
> > > > > thanks, but degrees of freedom goes to kinetic energies, still LJ
> > > > energies
> > > > > must be the same, yes?
> > > > >
> > > > >
> > > > > Best regards
> > > > >
> > > > >
> > > > > On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham <
> > > mark.j.abra...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > Your systems have different available degrees of freedom, so they
> > > > sample
> > > > > > difference spaces. The energies you observe reflect that
> > difference.
> > > > > >
> > > > > > Mark
> > > > > >
> > > > > > On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh 
> > > wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > I have a system containing of a virtual site of carbon
> connected
> > > > > > > symmetrically to two dummy massive sites (no charge). like :
> > > > M---C---M
> > > > > > > My problem is the results I get from simulation of this system
> is
> > > not
> > > > > > equal
> > > > > > > with results of single Carbon system simulation with mass of 2M
> > (at
> > > > > > exactly
> > > > > > > similar conditions)?
> > > > > > > They produce different LJ coul energies, I have even tried for
> > > > > > non-charged
> > > > > > > systems.
> > > > > > >
> > > > > > > Thank you in advance for help,
> > > > > > > Best regards
> > > > > > > --
> > > > > > > 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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> http://www.gromacs.org/Support/Mailing_Lists
> > > > > > >
> > > > > > > * For (un)subscribe requests visit
> > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> > gmx-users
> > > > or
> > > > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > > >
> > > > > > --
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> > > > > >
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> > > > > > Support/Mailing_Lists/GMX-Users_List before posting!
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> > > > > >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > or
> > > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > >
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> > > > > posting!
> > > > >
> > > > > * Can't post? Read 

Re: [gmx-users] virtual site connected to dummy massive site

[Faezeh Pousaneh]

Please note that the carbon is a virtual site, so has not mass. So the DOF
does not influence of its configurations on average. Besides the angle   of
M--C--M is always 180.

Mark, I compare the results of average distributions not a snapshot.

Justin, the only LJ are from atom C with next molecules in both systems.
(In fact I got the idea from your carbon dioxide tutorial, in which later I
will add two more virtual sites with charges to create a dipole moment for
my atom (e.g C here), but first I must understand this stage)



Best regards


On Sun, Nov 26, 2017 at 7:12 PM, Mark Abraham 
wrote:

> Hi,
>
> On Sun, Nov 26, 2017 at 6:35 PM Faezeh Pousaneh 
> wrote:
>
> > Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand
> my
> > question, I have no charges in systems on any atoms. So the extra DOF do
> > not effect on potential.
> >
>
> Charge has nothing to do with it. The potential is computed from all the
> interactions in the system, which in your case includes LJ. You aren't
> going to generate the same ensemble of configurations in your two cases, so
> you cannot expect to observe the same distribution of potential energy.
>
> Note that it would have been nice to say whether you were comparing a
> distribution of energies or a snapshot. As it is, we are guessing.
>
> Mark
>
> Best regards
> >
> >
> > On Fri, Nov 24, 2017 at 11:03 AM, Mark Abraham  >
> > wrote:
> >
> > > Hi,
> > >
> > > Potential energy is a function of configuration. You can expect the
> same
> > LJ
> > > energy if you compare the same configuration, ie that the distribution
> of
> > > states is identical. But if you would have the same total energy and a
> > > different distribution between PE and KE (because the DOF change) then
> > you
> > > will not sample the same states.
> > >
> > > Mark
> > >
> > > On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh 
> > > wrote:
> > >
> > > > Dear Mark,
> > > > thanks, but degrees of freedom goes to kinetic energies, still LJ
> > > energies
> > > > must be the same, yes?
> > > >
> > > >
> > > > Best regards
> > > >
> > > >
> > > > On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham <
> > mark.j.abra...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > Your systems have different available degrees of freedom, so they
> > > sample
> > > > > difference spaces. The energies you observe reflect that
> difference.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh 
> > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > I have a system containing of a virtual site of carbon connected
> > > > > > symmetrically to two dummy massive sites (no charge). like :
> > > M---C---M
> > > > > > My problem is the results I get from simulation of this system is
> > not
> > > > > equal
> > > > > > with results of single Carbon system simulation with mass of 2M
> (at
> > > > > exactly
> > > > > > similar conditions)?
> > > > > > They produce different LJ coul energies, I have even tried for
> > > > > non-charged
> > > > > > systems.
> > > > > >
> > > > > > Thank you in advance for help,
> > > > > > Best regards
> > > > > > --
> > > > > > 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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[gmx-users] Extending multidir simulations

[Joseph Brock]

Dear gmx community,

I would like to extend a simulation I ran using the mdrun -multidir option. 
Ideally, it would be good to extend .cpt files in all subdirectories 
simultaneously to make efficient use of a GPU node.

I looked here: 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
but it does not seem to cover the -multidir scenario. I could also not find any 
info about this searching the gmx-list archives and elsewhere on google. I am 
probably missing something very obvious, but if someone more experienced 
wouldn't mind pointing it out to me, I would be extremely grateful.

With thanks in advance,
-Joe.


Joseph Brock | PhD
Division of Physiological Chemistry II
Department of Medical Biochemistry and Biophysics
Karolinska Institutet
Scheeles väg 2
SE-171 77 Stockholm, Sweden

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Re: [gmx-users] version 16 of check point file

[Mark Abraham]

On Sun, Nov 26, 2017 at 2:05 PM rose rahmani  wrote:

> Hello;
>
> Which version of GROMACS use version 16 of check point file?
>

5.0 and all since.


> Is version 4.5.x of GROMACS use version 12 of check point file?
>

Yes

Mark


> Best Regards
> Rose
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Re: [gmx-users] Gromacs simulation with PEG

[Patrick Fuchs]

FYI, starting from GROMOS 53a6 parameters, we have refined them against 
the free energy of solvation of dimethoxyethane in water (and 
cyclohexane) (DOI: 10.1021/ct300245h). These new parameters are now part 
of the new 2016H66 force field (DOI: 10.1021/acs.jctc.6b00187).

Best,

Patrick

Le 12/11/2017 à 23:54, Dallas Warren a écrit :

You used the incorrect forcefield.

We have found that GROMOS53a6 and associated forcefields reproduce
poorly the interactions between PEG and water.  We have made
improvements on that, and will be publishing something soon.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 13 November 2017 at 09:51, Amali Guruge  wrote:

Dear Gromacs users,

I tried to simulate a system which contains PEG and water. According to the
phase diagram of PEG, it should form micells after the simulation. However,
after the simulation PEG doesn't form micells. What could be the reason for
this. Can anyone help me.

Thank you.
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Re: [gmx-users] virtual site connected to dummy massive site

[Mark Abraham]

Hi,

On Sun, Nov 26, 2017 at 6:35 PM Faezeh Pousaneh  wrote:

> Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand my
> question, I have no charges in systems on any atoms. So the extra DOF do
> not effect on potential.
>

Charge has nothing to do with it. The potential is computed from all the
interactions in the system, which in your case includes LJ. You aren't
going to generate the same ensemble of configurations in your two cases, so
you cannot expect to observe the same distribution of potential energy.

Note that it would have been nice to say whether you were comparing a
distribution of energies or a snapshot. As it is, we are guessing.

Mark

Best regards
>
>
> On Fri, Nov 24, 2017 at 11:03 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Potential energy is a function of configuration. You can expect the same
> LJ
> > energy if you compare the same configuration, ie that the distribution of
> > states is identical. But if you would have the same total energy and a
> > different distribution between PE and KE (because the DOF change) then
> you
> > will not sample the same states.
> >
> > Mark
> >
> > On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh 
> > wrote:
> >
> > > Dear Mark,
> > > thanks, but degrees of freedom goes to kinetic energies, still LJ
> > energies
> > > must be the same, yes?
> > >
> > >
> > > Best regards
> > >
> > >
> > > On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > Your systems have different available degrees of freedom, so they
> > sample
> > > > difference spaces. The energies you observe reflect that difference.
> > > >
> > > > Mark
> > > >
> > > > On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh 
> wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I have a system containing of a virtual site of carbon connected
> > > > > symmetrically to two dummy massive sites (no charge). like :
> > M---C---M
> > > > > My problem is the results I get from simulation of this system is
> not
> > > > equal
> > > > > with results of single Carbon system simulation with mass of 2M (at
> > > > exactly
> > > > > similar conditions)?
> > > > > They produce different LJ coul energies, I have even tried for
> > > > non-charged
> > > > > systems.
> > > > >
> > > > > Thank you in advance for help,
> > > > > Best regards
> > > > > --
> > > > > Gromacs Users mailing list
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Re: [gmx-users] Umbrella Sampling

[Justin Lemkul]

On 11/26/17 1:08 PM, Roja wrote:

Would you please tell me what is the difference between using umbrella in 4.5.x 
version and 5.1.4 version?are they different in ACCURACY of sampling?


Probably. There have been thousands of bug fixes and features added 
since 4.5.4, which was released 6 years ago. Refer to any and all of the 
release notes in the 4.5.x, 4.6.x, 5.0.x, 5.1.x, and 2016.x series. 
Again, the 4.5.x series is deprecated and officially unsupported.


-Justin


Sent from my iPhone


On Nov 26, 2017, at 21:14, Justin Lemkul  wrote:




On 11/26/17 12:40 PM, rose rahmani wrote:
Hello;

what re pull_ncoords , pull_coord1_type , pull_coord1_groups (in V5.1.4) called 
in version 4.5.4?

Why use deprecated software? We don't officially support the 4.5.x series any 
more. Use the newest version. Some things don't have exact equivalents because 
the pull code was completely re-written a few years ago.

-Justin

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==

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Virginia Tech Department of Biochemistry

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Re: [gmx-users] Umbrella Sampling

[Roja]

Would you please tell me what is the difference between using umbrella in 4.5.x 
version and 5.1.4 version?are they different in ACCURACY of sampling?

Sent from my iPhone

> On Nov 26, 2017, at 21:14, Justin Lemkul  wrote:
> 
> 
> 
>> On 11/26/17 12:40 PM, rose rahmani wrote:
>> Hello;
>> 
>> what re pull_ncoords , pull_coord1_type , pull_coord1_groups (in V5.1.4) 
>> called in version 4.5.4?
> 
> Why use deprecated software? We don't officially support the 4.5.x series any 
> more. Use the newest version. Some things don't have exact equivalents 
> because the pull code was completely re-written a few years ago.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> 
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> 
> ==
> 
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Re: [gmx-users] Umbrella Sampling

[Justin Lemkul]

On 11/26/17 12:40 PM, rose rahmani wrote:

Hello;

what re pull_ncoords , pull_coord1_type , pull_coord1_groups (in V5.1.4) called 
in version 4.5.4?


Why use deprecated software? We don't officially support the 4.5.x 
series any more. Use the newest version. Some things don't have exact 
equivalents because the pull code was completely re-written a few years ago.


-Justin

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] virtual site connected to dummy massive site

[Justin Lemkul]

On 11/26/17 12:34 PM, Faezeh Pousaneh wrote:

Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand my
question, I have no charges in systems on any atoms. So the extra DOF do
not effect on potential.


Maybe I (and others) are missing something here. We understand there are 
no charges, but that only affects the Coulombic energies. The LJ 
potentials of two systems are only the same if the interacting species 
have the same configuration. Do your virtual particles interact with 
anything via LJ? If they don't, I don't understand their purpose. You 
have to do an apples-to-apples comparison.


-Justin



Best regards


On Fri, Nov 24, 2017 at 11:03 AM, Mark Abraham 
wrote:


Hi,

Potential energy is a function of configuration. You can expect the same LJ
energy if you compare the same configuration, ie that the distribution of
states is identical. But if you would have the same total energy and a
different distribution between PE and KE (because the DOF change) then you
will not sample the same states.

Mark

On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh 
wrote:


Dear Mark,
thanks, but degrees of freedom goes to kinetic energies, still LJ

energies

must be the same, yes?


Best regards


On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham 
wrote:


Hi,

Your systems have different available degrees of freedom, so they

sample

difference spaces. The energies you observe reflect that difference.

Mark

On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh  wrote:


Hi,

I have a system containing of a virtual site of carbon connected
symmetrically to two dummy massive sites (no charge). like :

M---C---M

My problem is the results I get from simulation of this system is not

equal

with results of single Carbon system simulation with mass of 2M (at

exactly

similar conditions)?
They produce different LJ coul energies, I have even tried for

non-charged

systems.

Thank you in advance for help,
Best regards
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Virginia Tech Department of Biochemistry

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[gmx-users] Umbrella Sampling

[rose rahmani]

Hello;

what re pull_ncoords , pull_coord1_type , pull_coord1_groups (in V5.1.4) called 
in version 4.5.4?

Thank you so much
Rose
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Re: [gmx-users] virtual site connected to dummy massive site

[Faezeh Pousaneh]

Hi Mark, sorry I am not convinced yet. I hope you did not misunderstand my
question, I have no charges in systems on any atoms. So the extra DOF do
not effect on potential.


Best regards


On Fri, Nov 24, 2017 at 11:03 AM, Mark Abraham 
wrote:

> Hi,
>
> Potential energy is a function of configuration. You can expect the same LJ
> energy if you compare the same configuration, ie that the distribution of
> states is identical. But if you would have the same total energy and a
> different distribution between PE and KE (because the DOF change) then you
> will not sample the same states.
>
> Mark
>
> On Fri, Nov 24, 2017 at 10:56 AM Faezeh Pousaneh 
> wrote:
>
> > Dear Mark,
> > thanks, but degrees of freedom goes to kinetic energies, still LJ
> energies
> > must be the same, yes?
> >
> >
> > Best regards
> >
> >
> > On Fri, Nov 24, 2017 at 8:22 AM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Your systems have different available degrees of freedom, so they
> sample
> > > difference spaces. The energies you observe reflect that difference.
> > >
> > > Mark
> > >
> > > On Mon, 20 Nov 2017 18:18 Faezeh Pousaneh  wrote:
> > >
> > > > Hi,
> > > >
> > > > I have a system containing of a virtual site of carbon connected
> > > > symmetrically to two dummy massive sites (no charge). like :
> M---C---M
> > > > My problem is the results I get from simulation of this system is not
> > > equal
> > > > with results of single Carbon system simulation with mass of 2M (at
> > > exactly
> > > > similar conditions)?
> > > > They produce different LJ coul energies, I have even tried for
> > > non-charged
> > > > systems.
> > > >
> > > > Thank you in advance for help,
> > > > Best regards
> > > > --
> > > > 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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Re: [gmx-users] my modified residue falls apart after MD

[Justin Lemkul]

On 11/26/17 11:13 AM, MD wrote:

​Thank you Justin.

At the mean time I had another error after grompp, "ERROR 1 [file
topol_Protein_chain_E.itp, line 52165]:
   Unknown cmap torsion between atoms 3022 3024 3026 3046 3049"

the 3022 3024 3026 3046 3049 in the itp files referred to the backbone
(C-N-CA-C-N) of three connected residues R-W-T..


Double-check the atom types and make sure you haven't messed something 
up. Also note that your CSO residue needs a [cmap] directive like every 
other amino acid. If you've omitted it, add it.



I looked at the backbone of the pdb and it looks alright. this error didn't


This isn't a problem with geometry, so the PDB tells you nothing.


show up until today when i work from home using gromacs on another server.
DO you think if this is caused by different versions?


No idea, but do the scientific thing and maintain consistency so you can 
eliminate variables.


-Justin





On Sun, Nov 26, 2017 at 9:38 AM, Justin Lemkul  wrote:



On 11/26/17 9:32 AM, MD wrote:


Thank you Mark.

Do you think if the atom types of HE, OE and SG are correct in my
merged.rtp? These are the three atoms which have name changing cause of
the
inserted sulfur. I modified their atom types as well. I need to make sure
the type names are correct before I add the bond types in ffbonded.itp.


O is the carbonyl oxygen type in CHARMM, so I doubt that's a wise choice.
You may also need an entirely different sulfur atom type. Have you assessed
QM water interactions and dipole moments? Where did these charges come
from? If you haven't done so already, you need to do some really basic
validation before attempting to do anything with bonded parameters. The
dihedrals will be particularly sensitive to the quality of LJ and charge
terms.

-Justin


[ CSO ]

[ atoms ]
  N   NH1   -0.470  0
 HN H0.310  1
 CA   CT10.070  2
 HA   HB10.090  3
 CB   CT2   -0.110  4
HB1   HA20.090  5
HB2   HA20.090  6
 SG S0.67
 OE O   -0.83   8
 HE1H0.160  9
  C C0.510  10
  O O   -0.510 11
[ bonds ]
 CBCA
 SGCB
 SGOE
  NHN
  NCA
  CCA
  C+N
 CAHA
 CB   HB1
 CB   HB2
 OE   HE1
  O C


On Thu, Nov 23, 2017 at 12:25 AM, Mark Abraham 
wrote:

Hi,

You need to specify each bond you want, and for the types of those bonds
to
have parameters available. Bonds are specified with atoms, bond types are
specified with atom types.

Mark

On Thu, 23 Nov 2017 04:22 MD  wrote:

Yes. You are right about the names. I wrote them by memory and they were

not printed from the terminal. I will try to edit the ffbonded.itp and


see


how it goes. Thanks!
Ming

On Wed, Nov 22, 2017 at 10:14 PM, Justin Lemkul 
wrote:



On 11/22/17 10:11 PM, MD wrote:

​Justin, originally I did use SG and OE in the [bond​s] and I got

complaints of "SG-OE no default bond type" "CB SG OE" no default U-B


type
and "CT1, CT2, SG, OE" no default proper dihedral gypes. Are these the

Make sure you're clear on what needs to be done, because what you've

written above is not correct and would never be printed - your dihedral


is


a mix of types and names. All parameters are assigned by type, never by
name.

parameters you mean that are missing? If so, what files do you think I


should modify to create these parameters? ffbonded.itp, merged.rtp and
residuetype.dat?

ffbonded.itp


-Justin

On Wed, Nov 22, 2017 at 10:01 PM, Justin Lemkul 


wrote:

On 11/22/17 9:57 PM, MD wrote:

Thanks Justin. Then do I need to create new bond of SG and OE in


ff​bonded.itp? Cause I have tried adding SG and OE bond in


ffbonded.itp

and

SG and OE are atom names, not types. That's not a valid approach.


I got complaint from gromacs.. I modified the SG-OE bond from S-O


bond

and

it should work...

The [bonds] section requires atom names in order to function, so use


of

SG

and OE here is correct (your original entry used S and O, which are


atom

types and therefore not correct). If grompp subsequently complains

about

missing force field parameters when the correct bonds are written to

the

topology, then what you're attempting to do is not supported by the

force

field and you will have to either parametrize those missing

interactions

or

find parameters.

-Justin


On Wed, Nov 22, 2017 at 9:42 PM, Justin Lemkul 


wrote:

On 11/22/17 9:32 PM, MD wrote:

​Hi gromacs folks,

I was trying to introduce sulfenic acid as modified cysteine to
the

forcefield as following. Everything went well until the "gmx mdrun

-v

-deffnm em". The only file I modified was merged.rtp since there

were

no

new bond or dihedral angles. However my sulfenic acid falls apart
(oxygen
and sulfur are far away from the protein) after mdrun. Any help or
suggestions what I should do 

Re: [gmx-users] my modified residue falls apart after MD

[MD]

​Thank you Justin.

At the mean time I had another error after grompp, "ERROR 1 [file
topol_Protein_chain_E.itp, line 52165]:
  Unknown cmap torsion between atoms 3022 3024 3026 3046 3049"

the 3022 3024 3026 3046 3049 in the itp files referred to the backbone
(C-N-CA-C-N) of three connected residues R-W-T..
I looked at the backbone of the pdb and it looks alright. this error didn't
show up until today when i work from home using gromacs on another server.
DO you think if this is caused by different versions?



On Sun, Nov 26, 2017 at 9:38 AM, Justin Lemkul  wrote:

>
>
> On 11/26/17 9:32 AM, MD wrote:
>
>> Thank you Mark.
>>
>> Do you think if the atom types of HE, OE and SG are correct in my
>> merged.rtp? These are the three atoms which have name changing cause of
>> the
>> inserted sulfur. I modified their atom types as well. I need to make sure
>> the type names are correct before I add the bond types in ffbonded.itp.
>>
>
> O is the carbonyl oxygen type in CHARMM, so I doubt that's a wise choice.
> You may also need an entirely different sulfur atom type. Have you assessed
> QM water interactions and dipole moments? Where did these charges come
> from? If you haven't done so already, you need to do some really basic
> validation before attempting to do anything with bonded parameters. The
> dihedrals will be particularly sensitive to the quality of LJ and charge
> terms.
>
> -Justin
>
>
> [ CSO ]
>>[ atoms ]
>>  N   NH1   -0.470  0
>> HN H0.310  1
>> CA   CT10.070  2
>> HA   HB10.090  3
>> CB   CT2   -0.110  4
>>HB1   HA20.090  5
>>HB2   HA20.090  6
>> SG S0.67
>> OE O   -0.83   8
>> HE1H0.160  9
>>  C C0.510  10
>>  O O   -0.510 11
>>[ bonds ]
>> CBCA
>> SGCB
>> SGOE
>>  NHN
>>  NCA
>>  CCA
>>  C+N
>> CAHA
>> CB   HB1
>> CB   HB2
>> OE   HE1
>>  O C
>>
>>
>> On Thu, Nov 23, 2017 at 12:25 AM, Mark Abraham 
>> wrote:
>>
>> Hi,
>>>
>>> You need to specify each bond you want, and for the types of those bonds
>>> to
>>> have parameters available. Bonds are specified with atoms, bond types are
>>> specified with atom types.
>>>
>>> Mark
>>>
>>> On Thu, 23 Nov 2017 04:22 MD  wrote:
>>>
>>> Yes. You are right about the names. I wrote them by memory and they were
 not printed from the terminal. I will try to edit the ffbonded.itp and

>>> see
>>>
 how it goes. Thanks!
 Ming

 On Wed, Nov 22, 2017 at 10:14 PM, Justin Lemkul 
 wrote:


> On 11/22/17 10:11 PM, MD wrote:
>
> ​Justin, originally I did use SG and OE in the [bond​s] and I got
>> complaints of "SG-OE no default bond type" "CB SG OE" no default U-B
>>
> type

> and "CT1, CT2, SG, OE" no default proper dihedral gypes. Are these the
>>
>> Make sure you're clear on what needs to be done, because what you've
> written above is not correct and would never be printed - your dihedral
>
 is

> a mix of types and names. All parameters are assigned by type, never by
> name.
>
> parameters you mean that are missing? If so, what files do you think I
>
>> should modify to create these parameters? ffbonded.itp, merged.rtp and
>> residuetype.dat?
>>
>> ffbonded.itp
>
>
> -Justin
>
> On Wed, Nov 22, 2017 at 10:01 PM, Justin Lemkul 
>
 wrote:
>>>

>> On 11/22/17 9:57 PM, MD wrote:
>>>
>>> Thanks Justin. Then do I need to create new bond of SG and OE in
>>>
 ff​bonded.itp? Cause I have tried adding SG and OE bond in

>>> ffbonded.itp

> and

 SG and OE are atom names, not types. That's not a valid approach.

>>> I got complaint from gromacs.. I modified the SG-OE bond from S-O
>>>
>> bond
>>>
 and
>>>
>>> it should work...

 The [bonds] section requires atom names in order to function, so use

>>> of

> SG
>>> and OE here is correct (your original entry used S and O, which are
>>>
>> atom

> types and therefore not correct). If grompp subsequently complains
>>>
>> about

> missing force field parameters when the correct bonds are written to
>>>
>> the

> topology, then what you're attempting to do is not supported by the
>>>
>> force

> field and you will have to either parametrize those missing
>>>
>> interactions

> or
>>> find parameters.
>>>
>>> -Justin
>>>
>>>
>>> On Wed, Nov 22, 2017 at 9:42 PM, Justin Lemkul 
>>>
>> wrote:

> On 11/22/17 9:32 PM, MD wrote:

> ​Hi gromacs folks,
>
> I was trying to introduce 

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

[Rakesh Pant]

Dear Alex,

But g-x2top doesn't work till we define all atom types in .n2t file.

Thanks


On 26-Nov-2017 9:34 PM, "Alexandr Nasedkin"  wrote:

Hi,

You will need to have both ffbonded.itp and ffnonbonded.itp .

atomname2type.n2t is needed for g_x2top to make it work correctly.

Good luck.


-Alex



On 26/11/2017 10:52, Rakesh Pant wrote:

> Dear,  Alex
> Does it mean, we do not need to define all the atomtypes in the .nt2 file.
> It is enough to define all types in bonded and non-bonded itp.
>
> Thanks,
> Rakesh
>
>
>
>  Sent with Mailtrack
>  ral=rakesh.p...@students.iiserpune.ac.in=22>
>
> On Sun, Nov 26, 2017 at 3:27 PM, Alexandr Nasedkin 
> wrote:
>
> Edit the content of you ffnonbonded.itp file approximately this way:
>>
>> [ atomtypes ]
>> ;nameat.nummasschargeptypesigma epsilon
>> C1412.001.08A0.440000.63  ;
>> OCE815.999400-0.70A0.354000.159705  ; C-O-C
>> Bridging Oxygen;
>> OCH815.999400-0.51A0.354000.159705  ; C-O-H
>> Oxygen;
>>
>> HCO1 1.0080000.32A0.044900.235725  ; H-O-C
>> Hydrogen;
>> 
>>
>> You would need to search literature for respective ff parameters: all the
>> above parameters are taken from another topology to give a template.
>>
>>
>> -Alex
>>
>>
>> On 26/11/2017 10:37, Rakesh Pant wrote:
>>
>> Dear Alex,
>>>If I use O atoms to define the respective functional groups, then how
>>> to
>>> include the C atoms present in the molecule.
>>>
>>> Thanks,
>>> Rakesh
>>>
>>>
>>>
>>>  Sent with Mailtrack
>>> >> ral=rakesh.p...@students.iiserpune.ac.in=22>
>>>
>>> On Sun, Nov 26, 2017 at 3:08 PM, Alexandr Nasedkin >> >
>>> wrote:
>>>
>>> Hi,
>>>
 As I understood the problem, you need to distinguish between surface and
 buried carbons?

 You could define two atomtypes that differ in name and use it to process
 with x2top.

 Below is an example of *.n2t lines. You would need to change the charges
 and bondlengthes.

 ...

 OOCH-1.0515.99942C0.154 H 0.1; oxygen, -OH
 group
 OOCE-1.0515.99942C0.154 C 0.154; bridge
 oxygen

 ...

 Then you need *.n2t file in your ff.

 Good luck!


 -Alex


 On 25/11/2017 22:06, Justin Lemkul wrote:


 On 11/25/17 3:31 PM, Rakesh Pant wrote:
>
> But then I how will include the C atom (which is also one of the
>
>> atomtypes)?
>>
>> No idea, but I know people on this list have dealt with graphene oxide
>>
> before, so hopefully someone else chimes in.
>
> -Justin
>
>
> --
>
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Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

[Alexandr Nasedkin]

Hi,

You will need to have both ffbonded.itp and ffnonbonded.itp .

atomname2type.n2t is needed for g_x2top to make it work correctly.

Good luck.


-Alex


On 26/11/2017 10:52, Rakesh Pant wrote:

Dear,  Alex
Does it mean, we do not need to define all the atomtypes in the .nt2 file.
It is enough to define all types in bonded and non-bonded itp.

Thanks,
Rakesh



 Sent with Mailtrack


On Sun, Nov 26, 2017 at 3:27 PM, Alexandr Nasedkin 
wrote:


Edit the content of you ffnonbonded.itp file approximately this way:

[ atomtypes ]
;nameat.nummasschargeptypesigma epsilon
C1412.001.08A0.440000.63  ;
OCE815.999400-0.70A0.354000.159705  ; C-O-C
Bridging Oxygen;
OCH815.999400-0.51A0.354000.159705  ; C-O-H
Oxygen;

HCO1 1.0080000.32A0.044900.235725  ; H-O-C
Hydrogen;


You would need to search literature for respective ff parameters: all the
above parameters are taken from another topology to give a template.


-Alex


On 26/11/2017 10:37, Rakesh Pant wrote:


Dear Alex,
   If I use O atoms to define the respective functional groups, then how to
include the C atoms present in the molecule.

Thanks,
Rakesh



 Sent with Mailtrack


On Sun, Nov 26, 2017 at 3:08 PM, Alexandr Nasedkin 
wrote:

Hi,

As I understood the problem, you need to distinguish between surface and
buried carbons?

You could define two atomtypes that differ in name and use it to process
with x2top.

Below is an example of *.n2t lines. You would need to change the charges
and bondlengthes.

...

OOCH-1.0515.99942C0.154 H 0.1; oxygen, -OH
group
OOCE-1.0515.99942C0.154 C 0.154; bridge
oxygen

...

Then you need *.n2t file in your ff.

Good luck!


-Alex


On 25/11/2017 22:06, Justin Lemkul wrote:



On 11/25/17 3:31 PM, Rakesh Pant wrote:

But then I how will include the C atom (which is also one of the

atomtypes)?

No idea, but I know people on this list have dealt with graphene oxide

before, so hopefully someone else chimes in.

-Justin


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Re: [gmx-users] my modified residue falls apart after MD

[Justin Lemkul]

On 11/26/17 9:32 AM, MD wrote:

Thank you Mark.

Do you think if the atom types of HE, OE and SG are correct in my
merged.rtp? These are the three atoms which have name changing cause of the
inserted sulfur. I modified their atom types as well. I need to make sure
the type names are correct before I add the bond types in ffbonded.itp.


O is the carbonyl oxygen type in CHARMM, so I doubt that's a wise 
choice. You may also need an entirely different sulfur atom type. Have 
you assessed QM water interactions and dipole moments? Where did these 
charges come from? If you haven't done so already, you need to do some 
really basic validation before attempting to do anything with bonded 
parameters. The dihedrals will be particularly sensitive to the quality 
of LJ and charge terms.


-Justin


[ CSO ]
   [ atoms ]
 N   NH1   -0.470  0
HN H0.310  1
CA   CT10.070  2
HA   HB10.090  3
CB   CT2   -0.110  4
   HB1   HA20.090  5
   HB2   HA20.090  6
SG S0.67
OE O   -0.83   8
HE1H0.160  9
 C C0.510  10
 O O   -0.510 11
   [ bonds ]
CBCA
SGCB
SGOE
 NHN
 NCA
 CCA
 C+N
CAHA
CB   HB1
CB   HB2
OE   HE1
 O C


On Thu, Nov 23, 2017 at 12:25 AM, Mark Abraham 
wrote:


Hi,

You need to specify each bond you want, and for the types of those bonds to
have parameters available. Bonds are specified with atoms, bond types are
specified with atom types.

Mark

On Thu, 23 Nov 2017 04:22 MD  wrote:


Yes. You are right about the names. I wrote them by memory and they were
not printed from the terminal. I will try to edit the ffbonded.itp and

see

how it goes. Thanks!
Ming

On Wed, Nov 22, 2017 at 10:14 PM, Justin Lemkul  wrote:



On 11/22/17 10:11 PM, MD wrote:


​Justin, originally I did use SG and OE in the [bond​s] and I got
complaints of "SG-OE no default bond type" "CB SG OE" no default U-B

type

and "CT1, CT2, SG, OE" no default proper dihedral gypes. Are these the


Make sure you're clear on what needs to be done, because what you've
written above is not correct and would never be printed - your dihedral

is

a mix of types and names. All parameters are assigned by type, never by
name.

parameters you mean that are missing? If so, what files do you think I

should modify to create these parameters? ffbonded.itp, merged.rtp and
residuetype.dat?


ffbonded.itp


-Justin

On Wed, Nov 22, 2017 at 10:01 PM, Justin Lemkul 

wrote:



On 11/22/17 9:57 PM, MD wrote:

Thanks Justin. Then do I need to create new bond of SG and OE in

ff​bonded.itp? Cause I have tried adding SG and OE bond in

ffbonded.itp

and

SG and OE are atom names, not types. That's not a valid approach.

I got complaint from gromacs.. I modified the SG-OE bond from S-O

bond

and


it should work...

The [bonds] section requires atom names in order to function, so use

of

SG
and OE here is correct (your original entry used S and O, which are

atom

types and therefore not correct). If grompp subsequently complains

about

missing force field parameters when the correct bonds are written to

the

topology, then what you're attempting to do is not supported by the

force

field and you will have to either parametrize those missing

interactions

or
find parameters.

-Justin


On Wed, Nov 22, 2017 at 9:42 PM, Justin Lemkul 

wrote:

On 11/22/17 9:32 PM, MD wrote:

​Hi gromacs folks,


I was trying to introduce sulfenic acid as modified cysteine to

the

forcefield as following. Everything went well until the "gmx mdrun

-v

-deffnm em". The only file I modified was merged.rtp since there

were

no
new bond or dihedral angles. However my sulfenic acid falls apart
(oxygen
and sulfur are far away from the protein) after mdrun. Any help or
suggestions what I should do next? I am reading the manual at the

same

time
but I thought maybe I can get some help here as well.

Thank you for your time and any advice will be appreciated.

Ming

[ CSO ]
  [ atoms ]
N   NH1   -0.470  0
   HN H0.310  1
   CA   CT10.070  2
   HA   HB10.090  3
   CB   CT2   -0.110  4
  HB1   HA20.090  5
  HB2   HA20.090  6
   SG S0.67
   OE O   -0.83   8
   HE1H0.160  9
C C0.510  10
O O   -0.510 11
  [ bonds ]
   CBCA
   SCB
   SO
NHN
NCA
CCA
C+N
   CAHA
   CB   HB1
   CB   HB2
   OE   HE1
O C

You need a bond between SG and OE.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129

Re: [gmx-users] my modified residue falls apart after MD

[MD]

Thank you Mark.

Do you think if the atom types of HE, OE and SG are correct in my
merged.rtp? These are the three atoms which have name changing cause of the
inserted sulfur. I modified their atom types as well. I need to make sure
the type names are correct before I add the bond types in ffbonded.itp.

[ CSO ]
  [ atoms ]
N   NH1   -0.470  0
   HN H0.310  1
   CA   CT10.070  2
   HA   HB10.090  3
   CB   CT2   -0.110  4
  HB1   HA20.090  5
  HB2   HA20.090  6
   SG S0.67
   OE O   -0.83   8
   HE1H0.160  9
C C0.510  10
O O   -0.510 11
  [ bonds ]
   CBCA
   SGCB
   SGOE
NHN
NCA
CCA
C+N
   CAHA
   CB   HB1
   CB   HB2
   OE   HE1
O C


On Thu, Nov 23, 2017 at 12:25 AM, Mark Abraham 
wrote:

> Hi,
>
> You need to specify each bond you want, and for the types of those bonds to
> have parameters available. Bonds are specified with atoms, bond types are
> specified with atom types.
>
> Mark
>
> On Thu, 23 Nov 2017 04:22 MD  wrote:
>
> > Yes. You are right about the names. I wrote them by memory and they were
> > not printed from the terminal. I will try to edit the ffbonded.itp and
> see
> > how it goes. Thanks!
> > Ming
> >
> > On Wed, Nov 22, 2017 at 10:14 PM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 11/22/17 10:11 PM, MD wrote:
> > >
> > >> ​Justin, originally I did use SG and OE in the [bond​s] and I got
> > >> complaints of "SG-OE no default bond type" "CB SG OE" no default U-B
> > type
> > >> and "CT1, CT2, SG, OE" no default proper dihedral gypes. Are these the
> > >>
> > >
> > > Make sure you're clear on what needs to be done, because what you've
> > > written above is not correct and would never be printed - your dihedral
> > is
> > > a mix of types and names. All parameters are assigned by type, never by
> > > name.
> > >
> > > parameters you mean that are missing? If so, what files do you think I
> > >> should modify to create these parameters? ffbonded.itp, merged.rtp and
> > >> residuetype.dat?
> > >>
> > >
> > > ffbonded.itp
> > >
> > >
> > > -Justin
> > >
> > > On Wed, Nov 22, 2017 at 10:01 PM, Justin Lemkul 
> wrote:
> > >>
> > >>
> > >>> On 11/22/17 9:57 PM, MD wrote:
> > >>>
> > >>> Thanks Justin. Then do I need to create new bond of SG and OE in
> >  ff​bonded.itp? Cause I have tried adding SG and OE bond in
> > ffbonded.itp
> >  and
> > 
> >  SG and OE are atom names, not types. That's not a valid approach.
> > >>>
> > >>> I got complaint from gromacs.. I modified the SG-OE bond from S-O
> bond
> > >>> and
> > >>>
> >  it should work...
> > 
> >  The [bonds] section requires atom names in order to function, so use
> > of
> > >>> SG
> > >>> and OE here is correct (your original entry used S and O, which are
> > atom
> > >>> types and therefore not correct). If grompp subsequently complains
> > about
> > >>> missing force field parameters when the correct bonds are written to
> > the
> > >>> topology, then what you're attempting to do is not supported by the
> > force
> > >>> field and you will have to either parametrize those missing
> > interactions
> > >>> or
> > >>> find parameters.
> > >>>
> > >>> -Justin
> > >>>
> > >>>
> > >>> On Wed, Nov 22, 2017 at 9:42 PM, Justin Lemkul 
> > wrote:
> > >>>
> > 
> >  On 11/22/17 9:32 PM, MD wrote:
> > >
> > > ​Hi gromacs folks,
> > >
> > >> I was trying to introduce sulfenic acid as modified cysteine to
> the
> > >> forcefield as following. Everything went well until the "gmx mdrun
> > -v
> > >> -deffnm em". The only file I modified was merged.rtp since there
> > were
> > >> no
> > >> new bond or dihedral angles. However my sulfenic acid falls apart
> > >> (oxygen
> > >> and sulfur are far away from the protein) after mdrun. Any help or
> > >> suggestions what I should do next? I am reading the manual at the
> > same
> > >> time
> > >> but I thought maybe I can get some help here as well.
> > >>
> > >> Thank you for your time and any advice will be appreciated.
> > >>
> > >> Ming
> > >>
> > >> [ CSO ]
> > >>  [ atoms ]
> > >>N   NH1   -0.470  0
> > >>   HN H0.310  1
> > >>   CA   CT10.070  2
> > >>   HA   HB10.090  3
> > >>   CB   CT2   -0.110  4
> > >>  HB1   HA20.090  5
> > >>  HB2   HA20.090  6
> > >>   SG S0.67
> > >>   OE O   -0.83   8
> > >>   HE1H0.160  9
> > >>C C0.510  10
> > >>O O   -0.510 11
> > >>  [ bonds ]
> > >>   CBCA
> > >>   SCB
> > >>   SO
> > >>NHN
> > >>NCA
> > >>CCA
> > >>C+N
> > >>   CAHA
> > 

[gmx-users] version 16 of check point file

[rose rahmani]

Hello;

Which version of GROMACS use version 16 of check point file?
Is version 4.5.x of GROMACS use version 12 of check point file?

Best Regards
Rose
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Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

[Rakesh Pant]

Dear,  Alex
Does it mean, we do not need to define all the atomtypes in the .nt2 file.
It is enough to define all types in bonded and non-bonded itp.

Thanks,
Rakesh



 Sent with Mailtrack


On Sun, Nov 26, 2017 at 3:27 PM, Alexandr Nasedkin 
wrote:

> Edit the content of you ffnonbonded.itp file approximately this way:
>
> [ atomtypes ]
> ;nameat.nummasschargeptypesigma epsilon
> C1412.001.08A0.440000.63  ;
> OCE815.999400-0.70A0.354000.159705  ; C-O-C
> Bridging Oxygen;
> OCH815.999400-0.51A0.354000.159705  ; C-O-H
> Oxygen;
>
> HCO1 1.0080000.32A0.044900.235725  ; H-O-C
> Hydrogen;
> 
>
> You would need to search literature for respective ff parameters: all the
> above parameters are taken from another topology to give a template.
>
>
> -Alex
>
>
> On 26/11/2017 10:37, Rakesh Pant wrote:
>
>> Dear Alex,
>>   If I use O atoms to define the respective functional groups, then how to
>> include the C atoms present in the molecule.
>>
>> Thanks,
>> Rakesh
>>
>>
>>
>>  Sent with Mailtrack
>> > ral=rakesh.p...@students.iiserpune.ac.in=22>
>>
>> On Sun, Nov 26, 2017 at 3:08 PM, Alexandr Nasedkin 
>> wrote:
>>
>> Hi,
>>>
>>> As I understood the problem, you need to distinguish between surface and
>>> buried carbons?
>>>
>>> You could define two atomtypes that differ in name and use it to process
>>> with x2top.
>>>
>>> Below is an example of *.n2t lines. You would need to change the charges
>>> and bondlengthes.
>>>
>>> ...
>>>
>>> OOCH-1.0515.99942C0.154 H 0.1; oxygen, -OH
>>> group
>>> OOCE-1.0515.99942C0.154 C 0.154; bridge
>>> oxygen
>>>
>>> ...
>>>
>>> Then you need *.n2t file in your ff.
>>>
>>> Good luck!
>>>
>>>
>>> -Alex
>>>
>>>
>>> On 25/11/2017 22:06, Justin Lemkul wrote:
>>>
>>>
 On 11/25/17 3:31 PM, Rakesh Pant wrote:

 But then I how will include the C atom (which is also one of the
> atomtypes)?
>
> No idea, but I know people on this list have dealt with graphene oxide
 before, so hopefully someone else chimes in.

 -Justin


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>>>
>>>
>>
>>
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-- 
Rakesh Pant/राकेश पंत
Research Fellow/अनुसंधान फेलो
Indian Institute of Science Education and Research (IISER)
भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान
Pune-411008, India/ पुणे - ४११००८, भारत
Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm
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Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

[Alexandr Nasedkin]

Edit the content of you ffnonbonded.itp file approximately this way:

[ atomtypes ]
;name    at.num    mass        charge    ptype    sigma epsilon
C    14    12.00    1.08    A    0.44000        0.63      ;
OCE    8    15.999400    -0.70    A    0.35400        0.159705  ; C-O-C 
Bridging Oxygen;
OCH    8    15.999400    -0.51    A    0.35400        0.159705  ; C-O-H 
Oxygen;


HCO    1     1.008000    0.32    A    0.04490        0.235725  ; H-O-C 
Hydrogen;



You would need to search literature for respective ff parameters: all 
the above parameters are taken from another topology to give a template.



-Alex


On 26/11/2017 10:37, Rakesh Pant wrote:

Dear Alex,
  If I use O atoms to define the respective functional groups, then how to
include the C atoms present in the molecule.

Thanks,
Rakesh



 Sent with Mailtrack


On Sun, Nov 26, 2017 at 3:08 PM, Alexandr Nasedkin 
wrote:


Hi,

As I understood the problem, you need to distinguish between surface and
buried carbons?

You could define two atomtypes that differ in name and use it to process
with x2top.

Below is an example of *.n2t lines. You would need to change the charges
and bondlengthes.

...

OOCH-1.0515.99942C0.154 H 0.1; oxygen, -OH
group
OOCE-1.0515.99942C0.154 C 0.154; bridge oxygen

...

Then you need *.n2t file in your ff.

Good luck!


-Alex


On 25/11/2017 22:06, Justin Lemkul wrote:



On 11/25/17 3:31 PM, Rakesh Pant wrote:


But then I how will include the C atom (which is also one of the
atomtypes)?


No idea, but I know people on this list have dealt with graphene oxide
before, so hopefully someone else chimes in.

-Justin



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Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

[Rakesh Pant]

Dear Alex,
 If I use O atoms to define the respective functional groups, then how to
include the C atoms present in the molecule.

Thanks,
Rakesh



 Sent with Mailtrack


On Sun, Nov 26, 2017 at 3:08 PM, Alexandr Nasedkin 
wrote:

> Hi,
>
> As I understood the problem, you need to distinguish between surface and
> buried carbons?
>
> You could define two atomtypes that differ in name and use it to process
> with x2top.
>
> Below is an example of *.n2t lines. You would need to change the charges
> and bondlengthes.
>
> ...
>
> OOCH-1.0515.99942C0.154 H 0.1; oxygen, -OH
> group
> OOCE-1.0515.99942C0.154 C 0.154; bridge oxygen
>
> ...
>
> Then you need *.n2t file in your ff.
>
> Good luck!
>
>
> -Alex
>
>
> On 25/11/2017 22:06, Justin Lemkul wrote:
>
>>
>>
>> On 11/25/17 3:31 PM, Rakesh Pant wrote:
>>
>>> But then I how will include the C atom (which is also one of the
>>> atomtypes)?
>>>
>>
>> No idea, but I know people on this list have dealt with graphene oxide
>> before, so hopefully someone else chimes in.
>>
>> -Justin
>>
>>
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> * Please search the archive at http://www.gromacs.org/Support
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Rakesh Pant/राकेश पंत
Research Fellow/अनुसंधान फेलो
Indian Institute of Science Education and Research (IISER)
भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान
Pune-411008, India/ पुणे - ४११००८, भारत
Web:http://www.iiserpune.ac.in/~arun/webarun_files/rp.htm
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Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

[Alexandr Nasedkin]

Hi,

As I understood the problem, you need to distinguish between surface and 
buried carbons?


You could define two atomtypes that differ in name and use it to process 
with x2top.


Below is an example of *.n2t lines. You would need to change the charges 
and bondlengthes.


...

O    OCH    -1.05    15.9994    2    C    0.154 H 0.1    ; oxygen, -OH 
group

O    OCE    -1.05    15.9994    2    C    0.154 C 0.154    ; bridge oxygen

...

Then you need *.n2t file in your ff.

Good luck!


-Alex


On 25/11/2017 22:06, Justin Lemkul wrote:



On 11/25/17 3:31 PM, Rakesh Pant wrote:
But then I how will include the C atom (which is also one of the 
atomtypes)?


No idea, but I know people on this list have dealt with graphene oxide 
before, so hopefully someone else chimes in.


-Justin



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