Re: [gmx-users] Warning

[Quyen Vu]

Hi,
I think he got this warning due to he did not constraint the H-bond in his
simulation while he used a timestep of 2fs

On Mon, Jul 15, 2019 at 11:20 AM Mark Abraham 
wrote:

> Hi,
>
> As it says, your time step is too large to be a valid model of that bond
> interaction. Where did it come from?
>
> Mark
>
> On Mon., 15 Jul. 2019, 10:32 Bratin Kumar Das, <
> 177cy500.bra...@nitk.edu.in>
> wrote:
>
> > Dear All,
> >  I am getting the following error during running REMD
> > The bond in molecule-type Protein between atoms 49 OH and 50 HH has an
> >   estimated oscillational period of 9.0e-03 ps, which is less than 5
> times
> >   the time step of 2.0e-03 ps.
> >   Maybe you forgot to change the constraints mdp option.
> > What could be the reason.
> > --
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Re: [gmx-users] Topology for alphaketoglutarate to use in Gromacs

[Quyen Vu]

Hi,
For consistent with AMBER FF, you should follow this tutorial:
http://ambermd.org/tutorials/basic/tutorial4b/index.html
This will guide you to derive parameter to use with Amber engine  but, you
can easily convert them to Gromacs by using Acpype:
https://github.com/alanwilter/acpype
I have already had parameters of AKG at pH=7 (with partial charged derived
from QM calculation,HF/6-31G* and RESP fit), drop me a message if you want
Best,

On Thu, May 30, 2019 at 10:31 AM Pandya, Akash 
wrote:

> Hi,
>
> Can anyone guide me in generating Amber FF parameters for
> alphaketoglutarate to use in Gromacs? e.g. a tutorial?
>
> Best wishes,
>
> Akash
>
>
> Get Outlook for iOS
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Re: [gmx-users] Regarding Simulation

[Quyen Vu]

Hi,
That is normal, Gromacs writes checkpoint in case of your simulation crash
(electric power issue or time limit) so that Gromacs can continue the
simulation from the checkpoint. By default, 15min is the time interval of
writing checkpoint

On Sun, May 26, 2019 at 8:16 AM Omkar Singh 
wrote:

> Hello gromacs users,
> I am doing protein-water  simulation with calculating velocity. I am
> getting thins kind of checkpoint files,
>
> Energies (kJ/mol)
>G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
> 1.92508e+031.15716e+036.91130e+02   -1.22494e+021.70241e+04
> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.  Potential
> 9.37486e+04   -2.58204e+03   -6.26105e+051.62962e+03   -5.12634e+05
> Kinetic En.   Total Energy  Conserved En.Temperature Pres. DC (bar)
> 8.23638e+04   -4.30270e+05   -1.00795e+062.97016e+02   -1.27048e+02
>  Pressure (bar)   Constr. rmsd
>-1.49490e+022.24907e-05
>
> Writing checkpoint, step 89675360 at Sun May 26 08:34:47 2019
>
>
> Writing checkpoint, step 89679840 at Sun May 26 08:49:54 2019
>
>
> Writing checkpoint, step 89684160 at Sun May 26 09:04:53 2019
>
>
> Writing checkpoint, step 89688640 at Sun May 26 09:19:57 2019
>
>
> Writing checkpoint, step 89693200 at Sun May 26 09:34:45 2019
>
>
> Writing checkpoint, step 89697280 at Sun May 26 09:50:18 2019,
> Why it is happening? Can any tell?
> Thanks
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Re: [gmx-users] Multisite ion of Mg in Gromacs

[Quyen Vu]

Dear all,
Could anyone can please help me clarify the last paragraph on page 393 of
gromacs manual 2019.1?

"when sigma and epsilon need to be supplied (rule 2 and 3), it would seem
it is impossible to have non-zero C12 combined with a zero C6 parameter.
However, providing a negative sigma will do exactly that, such that C6 is
set to zero and C12 is calculated normally"

If the reference uses the potential function: U_{ij}=Aij/r_{ij}^12
-B_{ij}/r_{ij}^6 and provide A_i=0.05, B_i=0, how can I convert to epsilon
and sigma in Gromacs (using amber99sb force field)?
Thank you and best regards,


On Fri, May 24, 2019 at 12:15 PM Quyen Vu  wrote:

> Dear GMX users,
> I want to use multisite ion model for Mg2+ and I follow the parameters set
> of the paper: https://pubs.acs.org/doi/10.1021/jp501737x
> Here they develop these parameters for Q package. In the Lennard-Jones
> potentials, they use Aij, Bij terms (eq. 1) while Gromacs use epsilon and
> sigma term. The dummy atoms in their model have the repulsive term (Ai) but
> not attractive term (Bi=0).
>  How can I remove the attractive term of dummy atoms in Gromacs?
> Best regards,
> Quyen
>
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Re: [gmx-users] RMSD for specified length of DNA aptamer

[Quyen Vu]

Hi,
You should create an index file (use gmx make_ndx) that contains a list of
the atom you want to perform RMSD calculation on, e.g P atoms, or whatever
you want.
Then when you run gmx rms, you have to pass the index file from the above
step
Best,

On Sat, May 25, 2019 at 11:41 AM mmousivand93  wrote:

> Dear all
>
> I have been run molecular dynamic simulation between DNA(50bp)and small
> ligand,how to calculate RMSD value for
>
> specified length of DNA during 50ns simulation(for example  residues
> from 12 to 25)?
>
> Best Regards
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[gmx-users] Multisite ion of Mg in Gromacs

[Quyen Vu]

Dear GMX users,
I want to use multisite ion model for Mg2+ and I follow the parameters set
of the paper: https://pubs.acs.org/doi/10.1021/jp501737x
Here they develop these parameters for Q package. In the Lennard-Jones
potentials, they use Aij, Bij terms (eq. 1) while Gromacs use epsilon and
sigma term. The dummy atoms in their model have the repulsive term (Ai) but
not attractive term (Bi=0).
 How can I remove the attractive term of dummy atoms in Gromacs?
Best regards,
Quyen
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Re: [gmx-users] how to calculate binding energy using MMPBSA

[Quyen Vu]

There are many guides to do so, here is an example:
https://rashmikumari.github.io/g_mmpbsa/single_protein_ligand_binding_energy.html

On Wed, May 22, 2019 at 6:25 AM mmousivand93  wrote:

> Dear users
>
> I have run a MD simulation 50 ns and I am going to calculate the binding
> energy of DNA-ligand complex using MMPBSA, but I do not know how to do
> this, I appreciate any suggestion.
>
> Best Regards
>
> Maryam
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Re: [gmx-users] Fwd: atoms are not part of any of the T-Coupling groups

[Quyen Vu]

>From your mdp file, I guess you did not couple solvent and ions.
How many atoms in your system? and how many for protein, how many for
Urea_5ofprot

On Tue, May 7, 2019 at 7:41 AM ISHRAT JAHAN  wrote:

> -- Forwarded message -
> From: ISHRAT JAHAN 
> Date: Tue, May 7, 2019 at 11:05 AM
> Subject: atoms are not part of any of the T-Coupling groups
> To: 
>
>
> Dear all,
> I am trying to calculate the lennard Jones interaction energy between
> protein and urea in the first solvation shell. I have made the index group
> of urea molecule in the first solvation shell and then tried to generate
> the .tpr file using that index. After running the command
> gmx grompp -f full.mdp -p ../prot.top -c ../prot_u3M_200ns.tpr -o
> prot_u3M_rerun -n water_urea_5ofprot.ndx
> following error occur-
> 35099 atoms are not part of any of the T-Coupling groups
> part of  .mdp file and index file is given below
> rvdw=  1.2^M
> fourierspacing = 0.12^M
> fourier_nx = 0^M
> fourier_ny = 0^M
> fourier_nz = 0^M
> pme_order = 4^M
> ewald_rtol = 1e-5^M
> optimize_fft = yes^M
> ; Berendsen temperature coupling is on in two groups^M
> Tcoupl  =  V-rescale^M
> tc-grps =  Protein   Urea_5ofprot^M
> tau_t   =  0.10.1 ^M
> ref_t   =  300300   ^M
> ; Energy monitoring^M
> energygrps  =  Protein  Urea_5ofprot
> ; Isotropic pressure coupling is now on^M
> Pcoupl  =  berendsen^M
>  and at the end of the Index file i have only added the residue index of
> urea within 5 of protein and save the index file.
>
> [ Urea_5ofprot ]
> 1261 1262 1263 1264 1265 1266 1267 1268 1301 1302 1303 1304 1305 1306 1307
> 1308 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362
> 1363 1364 1413 1414 1415 1416 1417 1418 1419 1420 1501 1502 1503 1504 1505
> 1506 1507 1508 1517 1518 1519 1520 1521 1522 1523 1524 1581 1582 1583 1584
> 1585 1586 1587 1588 1637 1638 1639 1640 1641 1642 1643 1644 1685 1686 1687
> 1688 1689 1690 1691 1692 1725 1726 1727 1728 1729 1730 1731 1732 1741 1742
> 1743 1744 1745 1746 1747 1748 1773 1774 1775 1776 1777 1778 1779 1780 1781
> 1782 1783 1784 1785 1786 1787 1788 1797 1798 1799 1800 1801 1802 1803 1804
> 1893 1894 1895 1896 1897 1898 1899 1900 1933 1934 1935 1936 1937 1938 1939
> 1940 1989 1990 1991 1992 1993 1994 1995 1996 2021 2022 2023 2024 2025 2026
> 2027 2028 2253 2254 2255 2256 2257 2258 2259 2260 2269 2270 2271 2272 2273
> 2274 2275 2276 2285 2286 2287 2288 2289 2290 2291 2292 2333 2334 2335 2336
> 2337 2338 2339 2340 2341 2342 2343 2344 2345 2346 2347 2348 2365 2366 2367
> 2368 2369 2370 2371 2372 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502
> 2503 2504 2505 2506 2507 2508 2533 2534 2535 2536 2537 2538 2539 2540 2557
> 2558 2559 2560 2561 2562 2563 2564 2621 2622 2623 2624 2625 2626 2627 2628
> 2765 2766 2767 2768 2769 2770 2771 2772 2797 2798 2799 2800 2801 2802 2803
> 2804 2901 2902 2903 2904 2905 2906 2907 2908 2917 2918 2919 2920 2921 2922
> 2923 2924 2949 2950 2951 2952 2953 2954 2955 2956 3125 3126 3127 3128 3129
> 3130 3131 3132 3237 3238 3239 3240 3241 3242 3243 3244 3325 3326 3327 3328
> 3329 3330 3331 3332 3373 3374 3375 3376 3377 3378 3379 3380 3421 3422 3423
> 3424 3425 3426 3427 3428 3477 3478 3479 3480 3481 3482 3483 3484 3541 3542
> 3543 3544 3545 3546 3547 3548 3677 3678 3679 3680 3681 3682 3683 3684 3941
> 3942 3943 3944 3945 3946 3947 3948 3949 3950 3951 3952 3953 3954 3955 3956
> 3973 3974 3975 3976 3977 3978 3979 3980 4117 4118 4119 4120 4121 4122 4123
> 4124 4189 4190 4191 4192 4193 4194 4195 4196 4205 4206 4207 4208 4209 4210
> 4211 4212 4245 4246 4247 4248 4249 4250 4251 4252 4333 4334 4335 4336 4337
> 4338 4339 4340 4381 4382 4383 4384 4385 4386 4387 4388 4637 4638 4639 4640
> 4641 4642 4643 4644 4669 4670 4671 4672 4673 4674 4675 4676 4701 4702 4703
> 4704 4705 4706 4707 4708 4733 4734 4735 4736 4737 4738 4739 4740 4781 4782
> 4783 4784 4785 4786 4787 4788 4861 4862 4863 4864 4865 4866 4867 4868 4893
> 4894 4895 4896 4897 4898 4899 4900 4933 4934 4935 4936 4937 4938 4939 4940
> 5021 5022 5023 5024 5025 5026 5027 5028 5085 5086 5087 5088 5089 5090 5091
> 5092 5117 5118 5119 5120 5121 5122 5123 5124 5189 5190 5191 5192 5193 5194
> 5195 5196 5245 5246 5247 5248 5249 5250 5251 5252 5253 5254 5255 5256 5257
> 5258 5259 5260 5309 5310 5311 5312 5313 5314 5315 5316 5349 5350 5351 5352
> 5353 5354 5355 5356 5373 5374 5375 5376 5377 5378 5379 5380 5453 5454 5455
> 5456 5457 5458 5459 5460 5549 5550 5551 5552 5553 5554  5556 5565 5566
> 5567 5568 5569 5570 5571 5572 5581 5582 5583 5584 5585 5586 5587 5588 5669
> 5670 5671 5672 5673 5674 5675 5676 5693 5694 5695 5696 5697 5698 5699 5700
> 5813 5814 5815 5816 5817 5818 5819 5820 5901 5902 5903 5904 5905 5906 5907
> 5908 5949 5950 5951 5952 5953 5954 5955 5956 5973 5974 5975 5976 5977 5978
> 5979 5980 6005 6006 6007 6008 6009 6010 6011 6012 6061 6062 6063 6064 6065
> 6066 6067 6068 6253 6254 6255 6256 6257 

Re: [gmx-users] -ignh command removes protonation site of interest

[Quyen Vu]

Or another way to keep the protonated state of residue is using -asp, -glu,
-his ... and then you can manually assign the protonation state

On Tue, Apr 16, 2019 at 1:06 AM Justin Lemkul  wrote:

>
>
> On 4/15/19 6:30 PM, Neena Susan Eappen wrote:
> > Hello gromacs users,
> >
> > I started with a peptide where protonation site was on a carbonyl
> oxygen. However, using -ignh command in pdb2gmx, I lose that proton from
> there. Any insights on how to move forward?
>
> If you want another protonation state, then you need to make sure the
> residue is named as expected by the force field (e.g. ASPP for
> protonated aspartate, not ASP, etc).
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
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> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] Pulling simulation

[Quyen Vu]

Hi Naveen,
I think you are looking for absolute reference position in space, which is
mention on page 436 of manual 2019.1
In my case, I pull ACE residue.
my pulling code is:
pull= yes
pull_ncoords= 1 ; only one reaction coordinate
pull_ngroups= 1 ; two groups defining one reaction
coordinate
pull_coord1_groups  = 0 1
pull_group1_name= ACE
pull_coord1_type= umbrella  ; harmonic potential
pull_coord1_geometry= direction ; simple distance increase
pull-coord1-vec = 1.0 0.0 0.0
pull_coord1_dim = Y N N
pull_coord1_start   = yes   ; define initial COM distance > 0
pull-coord1-origin  = 18.0 5.19 5.06 ; absoulte reference point
pull_coord1_rate= 0.005  ; 0.005 nm per ps = 5 nm per ns
pull_coord1_k   = 600  ; kJ mol^-1 nm^-2
;*
Hope my code is useful with you or if I wrong, someone can correct me.
Best regards,
Quyen

On Mon, Apr 8, 2019 at 8:20 AM Naveen BK  wrote:

> Dear all,
>
> This question is regarding Umbrella sampling. My group 1 is substrate and
> group 2 protein. Trying to pull the substrate molecule from the active site
> pocket. In all the cases(for group 2), I used either atom or residue for
> the center of mass [COM]. Now I want to run a simulation by considering
> that COM of protein which may be present in the vacuum or in the empty
> space. In other words, I don't want to fix any atom or residue of the
> protein but I want to fix an empty space. I was not able to find any
> solutions regarding this if anyone could help me to figure it, would be
> great.
>
> --
> Thanks and Regards,
> Naveen Krishna
> +91 8123474717
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Re: [gmx-users] script

[Quyen Vu]

a dirty way:
grep -v ref_t npt.mdp >new.mdp && echo -e "ref_t=300" >>new.mdp
sorry again!


On Thu, Mar 7, 2019 at 6:16 PM Amin Rouy  wrote:

> It is fine.
> My question was not about '.mdp' itself. I meant how to define the
> 'Temperature' inside the bash scrip, to avoid changing it by opening the
> .mdp file.
>
>
> On Thu, Mar 7, 2019 at 4:57 PM Quyen Vu  wrote:
>
> > Dear all,
> > It's my fault that I have un-nice behavior, I'm so sorry for that.
> > If I understand correctly, you are working with Gromacs so you should
> > understand what is the .mdp file used for and there, the document of
> > temperature section talk about that.
> >
> >
> > On Thu, Mar 7, 2019 at 4:06 PM Amin Rouy  wrote:
> >
> > > Thank you Justin.
> > >
> > > Yes, Quyen I've read the manual. I got helps from Justin's scrips in
> his
> > > tutorial page (great source) and googled before I came to write here.
> > >
> > >
> > > On Thu, Mar 7, 2019 at 4:01 PM Justin Lemkul  wrote:
> > >
> > > >
> > > >
> > > > On 3/7/19 9:56 AM, Quyen Vu wrote:
> > > > > my question for you: have you ever read gromacs
> manual/documentation?
> > > >
> > > > Where in the GROMACS manual do we discuss how to use Linux commands
> to
> > > > alter scripts in this way? Please do not simply dismiss others'
> > > > questions; it is not productive and not helpful. There are legitimate
> > > > cases of users not utilizing documentation and web searching, but I
> > > > would argue this is not one of them.
> > > >
> > > > > On Thu, Mar 7, 2019 at 1:14 PM Amin Rouy 
> > > wrote:
> > > > >
> > > > >> Hi
> > > > >>
> > > > >> I would like to change the temperature of the simulation (NPT.mdp)
> > > > inside
> > > > >> my bash script, any one has idea?
> > > >
> > > > You can make replacements in files using standard Linux utilities
> like
> > > > sed, in conjunction with others like grep and awk. This isn't a
> > > > GROMACS-specific issue, so I'd suggest looking at more general Linux
> > > > forums.
> > > >
> > > > -Justin
> > > >
> > > > --
> > > > ==
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Assistant Professor
> > > > Office: 301 Fralin Hall
> > > > Lab: 303 Engel Hall
> > > >
> > > > Virginia Tech Department of Biochemistry
> > > > 340 West Campus Dr.
> > > > Blacksburg, VA 24061
> > > >
> > > > jalem...@vt.edu | (540) 231-3129
> > > > http://www.thelemkullab.com
> > > >
> > > > ==
> > > >
> > > > --
> > > > Gromacs Users mailing list
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Re: [gmx-users] script

[Quyen Vu]

Dear all,
It's my fault that I have un-nice behavior, I'm so sorry for that.
If I understand correctly, you are working with Gromacs so you should
understand what is the .mdp file used for and there, the document of
temperature section talk about that.


On Thu, Mar 7, 2019 at 4:06 PM Amin Rouy  wrote:

> Thank you Justin.
>
> Yes, Quyen I've read the manual. I got helps from Justin's scrips in his
> tutorial page (great source) and googled before I came to write here.
>
>
> On Thu, Mar 7, 2019 at 4:01 PM Justin Lemkul  wrote:
>
> >
> >
> > On 3/7/19 9:56 AM, Quyen Vu wrote:
> > > my question for you: have you ever read gromacs manual/documentation?
> >
> > Where in the GROMACS manual do we discuss how to use Linux commands to
> > alter scripts in this way? Please do not simply dismiss others'
> > questions; it is not productive and not helpful. There are legitimate
> > cases of users not utilizing documentation and web searching, but I
> > would argue this is not one of them.
> >
> > > On Thu, Mar 7, 2019 at 1:14 PM Amin Rouy 
> wrote:
> > >
> > >> Hi
> > >>
> > >> I would like to change the temperature of the simulation (NPT.mdp)
> > inside
> > >> my bash script, any one has idea?
> >
> > You can make replacements in files using standard Linux utilities like
> > sed, in conjunction with others like grep and awk. This isn't a
> > GROMACS-specific issue, so I'd suggest looking at more general Linux
> > forums.
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Office: 301 Fralin Hall
> > Lab: 303 Engel Hall
> >
> > Virginia Tech Department of Biochemistry
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalem...@vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==
> >
> > --
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Re: [gmx-users] script

[Quyen Vu]

my question for you: have you ever read gromacs manual/documentation?

On Thu, Mar 7, 2019 at 1:14 PM Amin Rouy  wrote:

> Hi
>
> I would like to change the temperature of the simulation (NPT.mdp) inside
> my bash script, any one has idea?
> thanks
> --
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Re: [gmx-users] position restraints on backbone: index error

[Quyen Vu]

So in my opinion, an easy way is separating each chain of your structure,
generate position restrain for them separately and then adding into
topology file of each chain

On Tue, Mar 5, 2019 at 1:18 PM Justin Lemkul  wrote:

>
>
> On 3/5/19 7:12 AM, morpheus wrote:
> > Thanks for your answer!
> >
> > I have followed your advice and generated the position restraint files
> for
> > each chain but it still comes up with an index error:
> >
> > ##
> > Fatal error:
> > [ file 2bnr_SLLDWITQV_dist_1.0.posre_Protein_chain_B.itp, line 5 ]:
> > Atom index (2975) in position_restraints out of bounds (1-).
> > ##
> >
> > What I have done was the following:
> >
> >
> > 1)  Create an index file from based on a pdb file that is the first frame
> > of the warming up procedure (where all atoms are position restrained (and
> > this works fine)):
> >
> > ##
> > make_ndx_mpi -f 2bnr_SLLDWITQV_dist_1.0.firstFrame.pr.pdb -o
> > 2bnr_SLLDWITQV_dist_1.0.indexForPositionRestraints.ndx
> >   chain A & 4
> >   chain B & 4
> >   chain C & 4
> >   chain D & 4
> >   chain E & 4
> > ##
> >
> >
> > 2) Create 1 itp file for each chain (example for chain A is given below):
> >
> > ##
> > genrestr_mpi -f 2bnr_SLLDWITQV_dist_1.0.pdb -n
> > 2bnr_SLLDWITQV_dist_1.0.indexForPositionRestraints.ndx -o
> > 2bnr_SLLDWITQV_dist_1.0.posre_Protein_chain_A.itp
> >11
> > ##
> >
> > 3) In the top file "2bnr_SLLDWITQV_dist_1.0_Protein_chain_A.itp" (and
> the 5
> > others) are included. They contain the indexes of all atoms. This file
> > looks like this:
> >
> > ##
> > [ moleculetype ]
> > ; Namenrexcl
> > Protein_chain_A 3
> >
> > [ atoms ]
> > ;   nr   type  resnr residue  atom   cgnr charge   mass
> > typeBchargeB  massB
> > ; residue   1 GLY rtp GLY  q +1.0
> >   1   MNH3  1GLYMN1  1  08.51535   ;
> > qtot 0
> >   2   MNH3  1GLYMN2  1  08.51535   ;
> > qtot 0
> >   3 NL  1GLY  N  1  0.129  0   ;
> > qtot 0.129
> >   4  H  1GLY H1  1  0.248  0   ;
> > qtot 0.377
> >   5  H  1GLY H2  1  0.248  0   ;
> > qtot 0.625
> >   6  H  1GLY H3  1  0.248  0   ;
> > qtot 0.873
> >   7CH2  1GLY CA  2  0.127 14.027   ;
> > qtot 1
> >   8  C  1GLY  C  3   0.45 12.011   ;
> > qtot 1.45
> >   9  O  1GLY  O  3  -0.4515.9994   ;
> > qtot 1
> > ; residue   2 SER rtp SER  q  0.0
> >  10  N  2SER  N  4  -0.3115.0147   ;
> > qtot 0.69
> >  11  H  2SER  H  4   0.31  0   ;
> > qtot 1
> >  12CH1  2SER CA  5  0 13.019   ;
> > qtot 1
> >  13CH2  2SER CB  6  0.266 14.027   ;
> > qtot 1.266
> > [...]
> > ; Include Position restraint file
> > #ifdef POSRES
> > #include "2bnr_SLLDWITQV_dist_1.0.posre_Protein_chain_A.itp"
> > #endif
> >
> >
> > or like this for chain B
> >
> >
> > [ moleculetype ]
> > ; Namenrexcl
> > Protein_chain_B 3
> >
> > [ atoms ]
> > ;   nr   type  resnr residue  atom   cgnr charge   mass
> > typeBchargeB  massB
> > ; residue   0 MET rtp MET  q +1.0
> >   1   MNH3  0METMN1  1  08.51535   ;
> > qtot 0
> >   2   MNH3  0METMN2  1  08.51535   ;
> > qtot 0
> >   3 NL  0MET  N  1  0.129  0   ;
> > qtot 0.129
> >   4  H  0MET H1  1  0.248  0   ;
> > qtot 0.377
> >   5  H  0MET H2  1  0.248  0   ;
> > qtot 0.625
> >   6  H  0MET H3  1  0.248  0   ;
> > qtot 0.873
> >   7CH1  0MET CA  2  0.127 13.019   ;
> > qtot 1
> >   8CH2  0MET CB  2  0 14.027   ;
> > qtot 1
> >   9CH2  0MET CG  3  0.241 14.027   ;
> > qtot 1.241
> >  10  S  0MET SD  3 -0.482  32.06   ;
> > qtot 0.759
> >  11CH3  0MET CE  3  0.241 15.035   ;
> > qtot 1
> >  12  C  0MET  C  4   0.45 12.011   ;
> > qtot 1.45
> >  13  O  0MET  O  4  -0.4515.9994   ;
> > qtot 1
> > ; residue   1 ILE rtp ILE  q  0.0
> >  14  N  1ILE  N  5  -0.3115.0147   ;
> > qtot 0.69
> >  15  H  1ILE  H  5   0.31  0   ;
> > qtot 1
> >  16CH1  1ILE CA  6  0 13.019   ;
> > 

Re: [gmx-users] position restraints on backbone: index error

[Quyen Vu]

Hi,
Position restraints are per molecule.
if you separate your molecule like that, the position restraints of
backbone should be generated for each chain base on indices of each chain
and include it in the topology of the chain, not global topology like that.
so for example, if you want restraint backbone of chain E, you have to
generate position restraint base on the topology of chain E and include him
in 2bnr_SLLDWITQV_dist_1.0_Protein_chain_E.itp

On Fri, Mar 1, 2019 at 10:53 AM morpheus 
wrote:

> Dear Gromacs users,
>
> I would like to run protein/protein interaction simulation (consisting of 5
> chains) that holds the backbone atoms rigid but allows side-chain
> movements. According to the Gromacs documentation this should work by:
>
> "Special position restraint .itp files can be created using the genrestr
> utility [...].  For example, if you wish to apply position restraints to
> only the backbone atoms of your protein, use genrestr and choose "Backbone"
> as the output group, and #include "backbone_posre.itp" in your topology."
> [1]
>
> I can generate the .itp file as described above but if I include it in my
> .top file then I get the following error:
>
> ###
> Fatal error:
> [ file backbone_posre.itp, line 687 ]:
> Atom index (2472) in position_restraints out of bounds (1-2471).
> This probably means that you have inserted topology section
> "position_restraints"
> in a part belonging to a different molecule than you intended to.
> In that case move the "position_restraints" section to the right molecule.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ###
>
>
> My top file looks like below and I have added the #include
> "backbone_posre.itp" part manually.
>
>
> ###
> ; Include forcefield parameters
> #include "gromos53a6.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "2bnr_SLLDWITQV_dist_1.0_Protein_chain_A.itp"
> #include "2bnr_SLLDWITQV_dist_1.0_Protein_chain_B.itp"
> #include "2bnr_SLLDWITQV_dist_1.0_Protein_chain_C.itp"
> #include "2bnr_SLLDWITQV_dist_1.0_Protein_chain_D.itp"
> #include "2bnr_SLLDWITQV_dist_1.0_Protein_chain_E.itp"
> #include "backbone_posre.itp"
>
> ; Include water topology
> #include "gromos53a6.ff/spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct   fcxfcyfcz
>11   1000   1000   1000
> #endif
>
> ; Include topology for ions
> #include "gromos53a6.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein in water
> ###
>
> What does "different molecule" mean in the error message? It should apply
> to all protein chains ... or in other words: what do I need to change to
> make this one run?
>
> Thanks!!
>
> M
>
>
> [1] http://www.gromacs.org/Documentation/How-tos/Position_Restraints
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Re: [gmx-users] avoid typing input

[Quyen Vu]

hope this help
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

On Wed, Feb 27, 2019 at 2:17 PM antonia vyrkou  wrote:

> hello,
>
> is there a way to execute an interactive gromacs command  (for example gmx
> rmsf , choosing a group number from an index file) without typing the
> number but "reading" it from a file or from a while loop?
> Does that make sense?
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Re: [gmx-users] How to use reduced unit in gromacs?

[Quyen Vu]

Have you checked gromacs manual? for example version of 2019.1 on page 299

On Wed, Feb 27, 2019 at 2:12 PM 이영규  wrote:

> Dear gromacs users,
>
> These days, I am working on supercritical fluid of lennard jones fluid. I
> want to make a system of supercritical fluid by using gromacs with reduced
> units. However, I am lost defining those parameters in gromacs. Could
> anyone help me to figure out this problem?
>
> Thanks in advance.
>
> Best regards
>
> --
>
> Yeongkyu Lee
>
> M.S student
>
> Department of Physics
>
> 501, Jinjudaero, Jinju, Gyeongnam
> <
> https://maps.google.com/?q=501,+Jinjudaero,+Jinju,+Gyeongnam=gmail=g
> >,
> 52828, Korea
>
> Email: monsterpl...@gmail.com
>
> Phone: +82-10-8771-2190
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Re: [gmx-users] Generating parameters of Alpha-Ketoglutarate for AMBER FF

[Quyen Vu]

usually, I use acpype to generate parameters for AKG and using Gaussian to
calculate partial charges

On Tue, Feb 26, 2019 at 2:33 PM Pandya, Akash 
wrote:

> Hi all,
>
> I am simulating my protein with Alpha-Ketoglutarate and I have been
> searching literature on ways to parameterise the molecule for the AMBER FF.
> I'm not having any luck and was wondering if anyone has or knows how to
> parameterise Alpha-Ketoglutarate? The chemical formula is C5H4O5-2.
>
> Any guidance will be much appreciated.
>
> Akash
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Re: [gmx-users] Interaction energies between atoms

[Quyen Vu]

As Mark mention, I also don't know what would I learn from its value but if
you want, you can define two groups, each group contains the index of the
atom that you want to calculate. In .mdp file, add this line: energygrps =
NAME_OF_GROUP_1 NAME_OF_GROUP_2

On Fri, Feb 15, 2019 at 10:36 AM Mark Abraham 
wrote:

> Hi,
>
> How would you define that interaction energy? What would you learn from its
> value?
>
> Mark
>
> On Fri, 15 Feb 2019 at 02:26 Sam David  wrote:
>
> > Hello GMX users,
> > I'm simulation a mixture of polymers, water, and hydrocarbons. I want to
> > calculate the interaction energies of an atom in one of the polymers with
> > another atom in the system.
> > Is there any way to do it in gromacs?
> >
> > Thank you
> > Sam
> > --
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Re: [gmx-users] Position restrained energy minimization

[Quyen Vu]

When you run EM with -v directive, you will see how much is the largest
force value applies to your atom. Try to estimate whether that force
constant was enough to keep your atom fix because if your structure has any
overlap, force can be very large

On Thu, Feb 7, 2019 at 6:40 AM Ashraya Ravikumar  wrote:

> Hi,
>
> I am trying to do position restrained energy minimization of a solvated
> peptide, where the peptide is restrained but the solvent is free to move.
> But I do see the positions of the atoms of the peptide change. I increased
> the force value in position restraint file to 1 from 1000, but it
> doesn't help. It is important for my analysis that the internal bond
> parameters (bond lengths, angles, and torsion angle) of the peptide do not
> change from its initial values. Is there any solution for this?
>
> Thanks in advance.
>
> Regards,
> Ashraya
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Re: [gmx-users] Calculate potential as function of time

[Quyen Vu Van]

Hi,
why don't you use gmx energy?
GROMACS online documents said: "gmx potential computes the electrostatical
potential across the box"

On Mon, Jan 21, 2019 at 7:53 AM Rituraj Purohit 
wrote:

> Hi Friends,
> How to get a  "graph of potential as function of time" ?? Currently I am
> using gmx potential script to generate potential.xvg but it is showing
> potential as function of boxlength.
> reg
> Rituraj
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Re: [gmx-users] perl water_deletor.pl

[Quyen Vu Van]

Hi,
I think you can write your script to delete it by defining the center of
liposome and  searching for water molecules in a range of hydrophobic
radius from that center
I suggest awk scripting language
Best,
Quyen

On Fri, Jan 18, 2019 at 9:30 AM rabee khorram 
wrote:

> *Hello everyone, *
> *I am running liposome structure with gromacs 5.*
> *this liposome created with Packmol software(without water molecules).*
> *after Solvating liposome with water in gromacs, I need to remove waters
> from hydrophobic region.*
>
> *is these  any "perl water_deletor.pl  " script
> for this structure?*
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Re: [gmx-users] Doubt about Steered molecular dynamics

[Quyen Vu Van]

Hi Justin,
What if I use the reference group is the absolute position in space by
specifying pull-coord1-origin: x0 y0 z0?
How about the force on this point now?
Thanks

On Thu, Jan 17, 2019 at 12:24 AM Justin Lemkul  wrote:

>
>
> On 1/16/19 6:22 PM, Quyen Vu Van wrote:
> > Hi Everyone,
> > Please help me to understand about COM Pulling in gromacs?
> > As I understand from Justin's tutorial, a dummy atom will be attached to
> > the center of mass of Protein A through a spring with a force constant of
> > 1000kJ / mol / nm ^ 2 (pull_coord1_k) and pulling along the positive
> > direction of the z-axis, dummy atom will move at a constant velocity
> > (pull_coord1_rate)
> > The pullf.xvg file contains the force that the spring acts on the center
> of
> > mass of Protein A, right?
> >
> > In the manual of gromacs says:
> > *pull_coord1_type = umbrella*
> >
> >
> > *A harmonic potential is applied between the centers of mass of two
> groups.
> > Thus, theforce is proportional to the displacement  *
> > What is the force in the manual means? Are two groups here Protein A and
> > Protein B or somewhat?
> > Is there any pulling force acts on Protein B?
>
> The force acts on the spring, which is then interpolated onto the
> specified groups.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] Doubt about Steered molecular dynamics

[Quyen Vu Van]

Sorry Justin,
Could you please explain in more details?
Thanks

On Thu, Jan 17, 2019 at 12:24 AM Justin Lemkul  wrote:

>
>
> On 1/16/19 6:22 PM, Quyen Vu Van wrote:
> > Hi Everyone,
> > Please help me to understand about COM Pulling in gromacs?
> > As I understand from Justin's tutorial, a dummy atom will be attached to
> > the center of mass of Protein A through a spring with a force constant of
> > 1000kJ / mol / nm ^ 2 (pull_coord1_k) and pulling along the positive
> > direction of the z-axis, dummy atom will move at a constant velocity
> > (pull_coord1_rate)
> > The pullf.xvg file contains the force that the spring acts on the center
> of
> > mass of Protein A, right?
> >
> > In the manual of gromacs says:
> > *pull_coord1_type = umbrella*
> >
> >
> > *A harmonic potential is applied between the centers of mass of two
> groups.
> > Thus, theforce is proportional to the displacement  *
> > What is the force in the manual means? Are two groups here Protein A and
> > Protein B or somewhat?
> > Is there any pulling force acts on Protein B?
>
> The force acts on the spring, which is then interpolated onto the
> specified groups.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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[gmx-users] Doubt about Steered molecular dynamics

[Quyen Vu Van]

Hi Everyone,
Please help me to understand about COM Pulling in gromacs?
As I understand from Justin's tutorial, a dummy atom will be attached to
the center of mass of Protein A through a spring with a force constant of
1000kJ / mol / nm ^ 2 (pull_coord1_k) and pulling along the positive
direction of the z-axis, dummy atom will move at a constant velocity
(pull_coord1_rate)
The pullf.xvg file contains the force that the spring acts on the center of
mass of Protein A, right?

In the manual of gromacs says:
*pull_coord1_type = umbrella*


*A harmonic potential is applied between the centers of mass of two groups.
Thus, theforce is proportional to the displacement  *
What is the force in the manual means? Are two groups here Protein A and
Protein B or somewhat?
Is there any pulling force acts on Protein B?

Thanks,
Quyen
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Re: [gmx-users] No pressure coupling in X direction

[Quyen Vu Van]

Dear Sam,
Thanks for your help.
Best


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On Wed, Jan 16, 2019 at 10:04 PM Sam David  wrote:

> Hi
> I have no idea about pull code but if you want pressure in a specific
> direction you can use anisotropic coupling where it has xx yy zz xy xz yz
> in your case xx=0, yy=p zz=p   xy=xz=yz=0
> check it online
>
> Best
>
>
>
> On Wed, Jan 16, 2019 at 1:50 PM Quyen Vu Van  wrote:
>
> > Dear all,
> > In pull code, I want to use *pull-coord1-geometry=direction-periodic* and
> > Gromacs requires no pressure coupling in the pulling direction, which is
> > x-direction in my case.
> > How can I just use pressure coupling for y-z direction?
> > Best regards,
> > Quyen
> > --
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[gmx-users] No pressure coupling in X direction

[Quyen Vu Van]

Dear all,
In pull code, I want to use *pull-coord1-geometry=direction-periodic* and
Gromacs requires no pressure coupling in the pulling direction, which is
x-direction in my case.
How can I just use pressure coupling for y-z direction?
Best regards,
Quyen
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[gmx-users] COM pulling: Reference position in space

[Quyen Vu Van]

Dear GMX community,
I read on manual of gromacs that the reference group in pulling code can be
defined by absolute position in space.

How can I change my setup for that purpose, for example the coordinate of
reference point X0 Y0 Z0
; Pull code
pull= yes
pull_ncoords= 1 ; only one reaction coordinate
pull_ngroups= 2 ; two groups defining one reaction
coordinate
pull_coord1_groups  = 1 2
pull_group1_name= ACE
pull_group2_name= CB50ALA
pull_coord1_type= umbrella  ; harmonic potential
pull_coord1_geometry= direction ; simple distance increase
pull-coord1-vec = -1.0 0.0 0.0
pull_coord1_start   = yes   ; define initial COM distance > 0
pull_coord1_rate= 0.005  ; 0.005 nm per ps = 5 nm per ns
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
Best regards,
Quyen
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Re: [gmx-users] bonded interaction larger than cutoff

[Quyen Vu Van]

Thanks Dr. Lumkel

On Mon, Dec 17, 2018 at 2:30 PM Justin Lemkul  wrote:

> On Mon, Dec 17, 2018 at 7:48 AM Quyen Vu Van  wrote:
>
> > Dear all,
> > I add a harmonic bond between two ends of my molecule (then my molecule
> > will have circle shape) with hope to calculate the force opens my
> molecule
> > (force the molecule straight).
> > Unfortunately, when this bond is quite big, gromacs said this bonded
> > interaction could not be calculated.
> > How can I overcome this? or is there any setup to calculate
> >
>
> Either do not use domain decomposition or use the pull code to bias the
> distance rather than trying to use a formal covalent bond.
>
> -Justin
> --
>
> ==
>
> Justin A. Lemkul, Ph.D.
>
> Assistant Professor
>
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
>
> ==
> --
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[gmx-users] bonded interaction larger than cutoff

[Quyen Vu Van]

Dear all,
I add a harmonic bond between two ends of my molecule (then my molecule
will have circle shape) with hope to calculate the force opens my molecule
(force the molecule straight).
Unfortunately, when this bond is quite big, gromacs said this bonded
interaction could not be calculated.
How can I overcome this? or is there any setup to calculate
Thanks and Best regards,
Quyen
<#m_-6527347489181658202_m_-7038046722413994203_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
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Re: [gmx-users] Nonbonded interaction between two molecules

[Quyen Vu Van]

Dear Justin
that's clear,
Thank you

On Tue, Nov 27, 2018 at 5:16 PM Justin Lemkul  wrote:

>
>
> On 11/27/18 11:14 AM, Quyen Vu Van wrote:
> > Dear Gromacs users,
> > I have a DNA molecule.
> > In PDB file two strands is separated by TER line, so pdb2gmx
> > separates my DNA as two molecules, each molecule has its topology file
> itp.
> > My question is whether the atoms in each strand have nonbonded
> interactions
> > with the other strand because as I understand that nonbonded interactions
> > are in [pairs] section in *.itp file
>
> Pairs define only 1-4 intramolecular nonbonded interactions. Everything
> else experiences nonbonded interactions based on which atoms fall within
> the nonbonded radius set in the .mdp file.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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[gmx-users] Nonbonded interaction between two molecules

[Quyen Vu Van]

Dear Gromacs users,
I have a DNA molecule.
In PDB file two strands is separated by TER line, so pdb2gmx
separates my DNA as two molecules, each molecule has its topology file itp.
My question is whether the atoms in each strand have nonbonded interactions
with the other strand because as I understand that nonbonded interactions
are in [pairs] section in *.itp file
Thank you and best regards
Quyen
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Re: [gmx-users] how to keep the ligand inside water box

[Quyen Vu Van]

Hi,
I don't know if there any way to keep ligand in the center of box but I
think you should apply the *position restraint* on the ligand in the
equilibrium process if you don't want the ligand move significantly

On Wed, Nov 14, 2018 at 1:08 PM Rahma Dahmani 
wrote:

> Hi GMX users,
>
> After running nvt equilibration, my ligand get out the box and before
> proceeding to npt equilibration i want to know how to get (and keep if is
> it possible) the ligand in water box* center* ?
>
> Thank you !
>
> --
>
>
>
>
>
>
> *Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des
> Matériaux à l'état condensé, Laboratoire de Chimie Théorique et
> Spectroscopie MoléculaireUniversité de Tunis El Manar, Faculté des Sciences
> de Tunis Campus Universitaire Farhat Hached - BP n ° 94 - Rommana 1068,
> Tunisie Tél: (+216) 28151042*
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Re: [gmx-users] Question about nsttcouple

[Quyen Vu Van]

nsttcouple=10 means that nsstcouple*dt(2fs, I guess)=0.02 and your
tau-t=0.1 (5 fold)
when nsttcouple=20, nsstcouple*dt=0.04 so your tau-t is only 2.5 fold. I
think so

On Wed, Nov 7, 2018 at 3:43 PM minky son  wrote:

> Dear gmx users,
>
>
> In gromacs manual,
>
> “nsttcouple: The default value of -1 sets nsttcouple equal to nstlist,
> unless nstlist <=0, then a value of 10 is used.”
>
>
>
> When I did grompp with the following mdp options,
>
> nstlist = 20
>
> tcoupl = berendsen
>
> nsttcouple = -1
>
> tau-t = 0.1
>
>
>
> I got a warning message.
>
> WARNING 1 [file pr_nvt.mdp]:
>
>   "For proper integration of the Berendsen thermostat, tau-t (0.1) should
> be at least 5 times larger than nsttcouple*dt (0.04)"
>
>
>
> I think this means that nsttcouple is applied to 20, not 10. This doesn't
> match with the one mentioned in the manual. why?
>
>
>
>
>
> When I also tried nstlist=10, grompp didn’t show any warning.
>
> But the value of nstlist was automatically changed to 40 in mdrun.
>
> Is nsttcouple applied to 10 in this case?
>
>
>
> Please give me an advice.
>
> Thank you.
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Re: [gmx-users] Turn on/off residues in gromacs

[Quyen Vu Van]

Dear Justin,
Anyway, thank you so much

On Sat, Nov 3, 2018, 17:27 Justin Lemkul 
>
> On 11/1/18 5:41 PM, Quyen Vu Van wrote:
> > Dear Justin,
> > Could you please give me comments about the Mimicking nascent peptide
> > elongation part in the Materials and Methods section of this paper:
> > https://www.nature.com/articles/s41598-018-24344-9
> > Thank you so much
>
> I don't have time to review papers to help you do your work, sorry. But
> any approach that leaves unsatisfied valences is suspect in my mind, and
> I have already expressed my opinion about such approaches.
>
> -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.thelemkullab.com
>
> ==
>
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Re: [gmx-users] Turn on/off residues in gromacs

[Quyen Vu Van]

Dear Justin,
Could you please give me comments about the Mimicking nascent peptide
elongation part in the Materials and Methods section of this paper:
https://www.nature.com/articles/s41598-018-24344-9
Thank you so much
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Re: [gmx-users] Turn on/off residues in gromacs

[Quyen Vu Van]

Dear Justin,
Thanks for your respond.
What if I mean turn off residues just by remove the non-bonded term and
then gradually adding non-bonded interactions back?
Best regards,
Quyen

On Mon, Oct 22, 2018, 14:11 Justin Lemkul  wrote:

>
>
> On 10/22/18 7:29 AM, Quyen Vu Van wrote:
> > Dear all,
> > sorry for my unclear question,
> > I attached here the quick draw picture of what I am saying, please take a
> > look: https://www.dropbox.com/s/eycsm3qsywhgxjv/model.pdf?dl=0
>
> What you are trying to do is both technically challenging and physically
> questionable. The free energy options allow you to modulate the
> interactions of a [moleculetype] with the remainder of the system; you
> can't easily decompose individual residues of a protein, which is part
> of a single [moleculetype]. You could manually define A- and B- states
> in the topology and there are various tools to do that.
>
> The bigger problem is, even if you accomplish what you seek in terms of
> the technical setup, it's physically unrealistic. As Mark noted, you
> have an unsatisfied valence at the C-terminus of each residue at each
> interval of time. This is not physically real, as amino acids are simply
> transferred between tRNA and onto the growing polypeptide chain. Simply
> "growing" residues onto the chain will not come close to mimicking
> protein synthesis in any meaningful way.
>
> -Justin
>
> > Thank you and best regards,
> > Quyen
> >
> > On Sat, Oct 20, 2018 at 6:27 AM Quyen Vu Van 
> wrote:
> >
> >> Dear Mark,
> >> I mean that e.g my protein has 10 residues in pdb file but at t=0,
> Gromacs
> >> will only calculate the interactions of all atoms in residue 1
> >> t= 1ns (for example) Gromacs will calculate the interactions of all
> atoms
> >> in residues 1 and 2, and so on till t= XXX ns, interactions of all
> atoms of
> >> full protein is take into account.
> >> Best regards,
> >> Quyen
> >>
> >>
> >> On Fri, Oct 19, 2018, 18:42 Mark Abraham 
> wrote:
> >>
> >>> Hi,
> >>>
> >>> What do you mean by turning a residue off? What would terminate the
> >>> chemical bond to the residue that it was bound to?
> >>>
> >>> Mark
> >>>
> >>> On Fri, Oct 19, 2018, 14:40 Quyen Vu Van  wrote:
> >>>
> >>>> Dear Gromacs community,
> >>>> How can I turn off/on residues in the protein, I want to mimic the
> >>> process
> >>>> of protein synthesis.
> >>>> Thank you and best regards,
> >>>> Quyen
> >>>> --
> >>>> 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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> >>>>
> >>> --
> >>> Gromacs Users mailing list
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> >>>
>
> --
> ==
>
> 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.thelemkullab.com
>
> ==
>
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Re: [gmx-users] Turn on/off residues in gromacs

[Quyen Vu Van]

Dear all,
sorry for my unclear question,
I attached here the quick draw picture of what I am saying, please take a
look: https://www.dropbox.com/s/eycsm3qsywhgxjv/model.pdf?dl=0
Thank you and best regards,
Quyen

On Sat, Oct 20, 2018 at 6:27 AM Quyen Vu Van  wrote:

> Dear Mark,
> I mean that e.g my protein has 10 residues in pdb file but at t=0, Gromacs
> will only calculate the interactions of all atoms in residue 1
> t= 1ns (for example) Gromacs will calculate the interactions of all atoms
> in residues 1 and 2, and so on till t= XXX ns, interactions of all atoms of
> full protein is take into account.
> Best regards,
> Quyen
>
>
> On Fri, Oct 19, 2018, 18:42 Mark Abraham  wrote:
>
>> Hi,
>>
>> What do you mean by turning a residue off? What would terminate the
>> chemical bond to the residue that it was bound to?
>>
>> Mark
>>
>> On Fri, Oct 19, 2018, 14:40 Quyen Vu Van  wrote:
>>
>> > Dear Gromacs community,
>> > How can I turn off/on residues in the protein, I want to mimic the
>> process
>> > of protein synthesis.
>> > Thank you and best regards,
>> > Quyen
>> > --
>> > 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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>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>
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Re: [gmx-users] Turn on/off residues in gromacs

[Quyen Vu Van]

Dear Mark,
I mean that e.g my protein has 10 residues in pdb file but at t=0, Gromacs
will only calculate the interactions of all atoms in residue 1
t= 1ns (for example) Gromacs will calculate the interactions of all atoms
in residues 1 and 2, and so on till t= XXX ns, interactions of all atoms of
full protein is take into account.
Best regards,
Quyen


On Fri, Oct 19, 2018, 18:42 Mark Abraham  wrote:

> Hi,
>
> What do you mean by turning a residue off? What would terminate the
> chemical bond to the residue that it was bound to?
>
> Mark
>
> On Fri, Oct 19, 2018, 14:40 Quyen Vu Van  wrote:
>
> > Dear Gromacs community,
> > How can I turn off/on residues in the protein, I want to mimic the
> process
> > of protein synthesis.
> > Thank you and best regards,
> > Quyen
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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[gmx-users] Turn on/off residues in gromacs

[Quyen Vu Van]

Dear Gromacs community,
How can I turn off/on residues in the protein, I want to mimic the process
of protein synthesis.
Thank you and best regards,
Quyen
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Re: [gmx-users] How to evaluate the Hbond and non-bonded interactions between ligand-receptor

[Quyen Vu Van]

The second column is interactions which satisfy both angle and distance
cutoff of hydrogen bond. The third column is just interaction satisfy
distance cutoff

On Sun, Aug 26, 2018, 23:03 mmousivand93  wrote:

> Dear all users
>
> Hi, I have run molecular dynamic for SSDNA-Ligand (50ns), I am going to
> determin the most efficient interactions(the Hbond and non-bonded
> interactions )  observed during 50 ns molecular dynamic simulations in
> ssDNA-ligand complex. Using hbond command in gromacs I have see only
> the number of hydrogen bond,however I do not know what the second and
> third columns represent in hbond.xvg?I used the following command for
> Hbond analysis: HBOND –F trp_md.xtc –S trp_md.tpr –NUM trp_hnum.xvg
>
> Best regards
>
> Maryam
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