[gmx-users] Regarding parameters for Bromine ion in Charmm36 FF
Hello all, In charmm36 FF of gromacs among the halogens only chlorine ion (Cl-) parameter is defined but parameters for Fluorine (F-), Bromine (Br-), Iodine (I-) anions are not defined. So, can anybody kindly help regarding getting the parameters of Fluorine (F-), Bromine (Br-), Iodine (I-) anions in charmm36 FF...? Any suggestions are highly appreciated. Thank you. --- With Best Regards, *Dilip.H.N* Ph.D Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 13/03/20, 12:46:30 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
[gmx-users] Cannot flush logfile - maybe you are out of disk space?
Dear all, I have extended a simulation (extension for 50 ns) and after some time i get the following error "Cannot flush logfile - maybe you are out of disk space?" and now the simulation has stopped running. The log file of the simulation is stopped at say 83ns- Step Time 4156600083132.0 Now i have made the disk-free and still, the simulation is still struck. So now may i know how can i proceed..?? Any suggestions are highly appreciated. Thank you. --- With Best Regards, *Dilip.H.N* Ph.D Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 17/02/20, 12:14:16 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
Re: [gmx-users] Amide hydrogen naming in charmm 36 forcefield
Sir, I have also tried with atom name H, (i have checked in the .rtp file and is named as 'H'), but still i am getting the same following error: Atom HN in residue NMA 1 was not found in rtp entry NMA with 12 atoms while sorting atoms. First, i tried with naming the amide hydrogens as 'H' and got the above-mentioned error and then i followed the link https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-May/088942.html which stated "CHARMM has unique nomenclature for amide H atoms, so H needs to be renamed HN, though unfortunately, that's also wrong in the .rtp file. I'll fix that for the future." and hence i changed the 'H' into 'HN'. In spite in both the cases (naming the amide hydrogens as 'H' or 'HN'), i am getting the errors. The amide nitrogens are not defined in the .hdb files in charmm36 FF too. Any suggestions...? Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 20/07/19, 10:34:20 On Sat, Jul 20, 2019 at 5:30 AM Justin Lemkul wrote: > > > On 7/19/19 9:26 AM, Dilip.H.N wrote: > > Hello, > > I tried to get the topology for the N-methyl acetamide (NMA) through gmx > > pdb2gmx command in charmm 36 FF, > > but the following error states: > > > > Atom HN in residue NMA 1 was not found in rtp entry NMA with 12 atoms > > while sorting atoms. > > For a hydrogen, this can be a different protonation state, or it > > might have had a different number in the PDB file and was rebuilt > > (it might for instance have been H3, and we only expected H1 & H2). > > Note that hydrogens might have been added to the entry for the > N-terminus. > > Remove this hydrogen or choose a different protonation state to solve it. > > Option -ignh will ignore all hydrogens in the input. > > > > When searched i found the following link > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-May/088942.html > > > > which states that "CHARMM has unique nomenclature for amide H > > atoms,.." as stated by Dr. Justin lemkul. Even in the .hdb file, > > the naming has not been addressed. > > I have tried renaming the amide hydrogen into 'HN' from 'H' but still > gives > > the error. Why is this amide hydrogen unnamed in Charmm 36 FF...? > > > > So, May i know has this issue been resolved? > > The atom name is H. Check the NMA entry in the .rtp file and you will > see this. > > -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 > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read 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. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
[gmx-users] Amide hydrogen naming in charmm 36 forcefield
Hello, I tried to get the topology for the N-methyl acetamide (NMA) through gmx pdb2gmx command in charmm 36 FF, but the following error states: Atom HN in residue NMA 1 was not found in rtp entry NMA with 12 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 & H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. When searched i found the following link https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-May/088942.html which states that "CHARMM has unique nomenclature for amide H atoms,.." as stated by Dr. Justin lemkul. Even in the .hdb file, the naming has not been addressed. I have tried renaming the amide hydrogen into 'HN' from 'H' but still gives the error. Why is this amide hydrogen unnamed in Charmm 36 FF...? So, May i know has this issue been resolved? How can i solve this problem? Any suggestions are appreciated. Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 19/07/19, 18:49:04 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
[gmx-users] Relative constraint deviation after LINCS:
Hi all, I am running a simulation of peptide and during the course of the simulation after some steps, the simulation gets canceled stating the following message: Step 1848418, time 3696.84 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.08, max 0.000547 (between atoms 5577 and 5578) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5577 5578 47.60. 0.1110 0. Step 1848419, time 3696.84 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.17, max 0.001112 (between atoms 5577 and 5580) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5577 5578 39.90.1110 0. 0. Step 1848420, time 3696.84 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.24, max 0.001800 (between atoms 5577 and 5580) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5577 5578 30.20. 0. 0. Step 1848421, time 3696.84 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.34, max 0.002419 (between atoms 5577 and 5580) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length /var/spool/slurmd/job29017/slurm_script: line 11: 91791 Segmentation fault gmx_mpi_d mdrun -v -s nvtmdd.tpr -deffnm nvtmdd Why is this happening..?? Any suggestions on how can i resolve this issue..? Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 05/07/19, 09:58:23 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
[gmx-users] Broken bonds between peptide and capped terminals when solvated
Hi all, I have a capped peptide and when i solvate the system with water and visualize it in vmd, the bonds between the peptide and corresponding capped N and C terminal groups is not seen (or) broken. Whereas before solvating the system, the bonds between the peptide and corresponding capped N and C terminals are intact when visualized in vmd. Why is this happening? After solvating the peptide system, why are the bonds between peptide and capped terminal groups getting broken.? How can i solve this issue...? Any suggestions are highly appreciated. Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 27/05/19, 10:33:05 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
[gmx-users] Unusual bond between residues which are capped
Hi all, I have a peptide which is capped on the N-terminal and C-terminal with acetyl and N-methyl groups. But when i view this in vmd, i get the following error as: Warning) Unusual bond between residues: 1 (none) and 2 (protein) Warning) Unusual bond between residues: 8 (protein) and 9 (none) Warning) Unusual bond between residues: 1 (none) and 2 (protein) Warning) Unusual bond between residues: 8 (protein) and 9 (none) Warning) Unusual bond between residues: 1 (none) and 2 (protein) Warning) Unusual bond between residues: 8 (protein) and 9 (none) Here 1 (none) is the acetyl group and 9 (none) is the N-methyl group which are capped to the protein C and N terminals. How can i solve this issue..?? Any suggestions? Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 27/05/19, 10:24:16 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
[gmx-users] Different models of TMAO
Hello all, I have run a simulation with TMAO using Charmm36 FF and i want to see whether different models of TMAO ie., Kast, Netz and Garcia models do solvate/behave in the same way. So, can anybody share the relevant parameter files as .rtp, .itp etc., of the above mentioned three different TMAO models required to run the simulations... How can i include the epsilon and LJ parameters in it...? Any suggestions are appreciated. Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 20/03/19, 20:54:23 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
[gmx-users] Different models of TMAO
Hello all, I have run a simulation with TMAO using Charmm36 FF and i want to see whether different models of TMAO ie., Kast, Netz and Garcia models do solvate/behave in the same way. So, can anybody share the relevant parameter files as .rtp, .itp etc., of the above mentioned three different TMAO models required to run the simulations... Any suggestions are appreciated. Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 19/03/19, 12:40:53 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
[gmx-users] Residue id of capped peptide getting changed when adding molecules
Hi, I have a capped peptide (ACE-ALA-NME) and now when i add the other molecules through the command "gmx insert-molecules", the residue id of the capped peptide, which was 1 as: 1ACECH3 1ACE HH31 1ACE HH32 1ACE HH33 1ACE C 1ACE O 1ALA N 1ALA HN 1ALA CA 1ALA HA 1ALA CB 1ALAHB1 1ALAHB2 1ALAHB3 1ALA C 1ALA O 1NME N 1NME HN 1NMECH3 1NME HH31 1NME HH32 1NME HH33 gets changed to 1,2 and 3 as in: 1ACECH3 1ACE HH31 1ACE HH32 1ACE HH33 1ACE C 1ACE O 2ALA N 2ALA HN 2ALA CA 2ALA HA 2ALA CB 2ALAHB1 2ALAHB2 2ALAHB3 2ALA C 2ALA O 3NME N 3NME HN 3NMECH3 3NME HH31 3NME HH32 3NME HH33 4XYZ N1 4XYZ N2 4XYZ C1 and so on... 1] How can i prevent the residue id's from getting changed..??(or) retain their residue id's..? 2] Since when residue id's gets changed, it is treated as different chains/molecules and bonds between them are shown as "Warning) Unusual bond between residues: 1(none) and 2 (protein) Warning) Unusual bond between residues: 2 (protein) and 3 (none)" when viewed in VMD. causing a problem... Any suggestions are highly appreciated. Thank you. --- With Best Regards, Dilip.H.N Ph.D. Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 15/11/18, 11:02:34 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
[gmx-users] Regarding rigidity of water models
Hello all, I have done a simulation with amino-aid+cosolvent+water in which for the amino-acid and co-solvent i have used charmm36 FF and SPC model for water. I have a few Doubts:- 1) Is this SPC water model which i have used is suitable in case of charmm36ff..?? Referring to Justin's answer in RG-- https://www.researchgate.net/post/What_is_differences_between_tip3p_and_tips3p_water_model 2) From the literature, it states that the SPC, SPC/E, TIP3P etc are rigid models. If then is there any stretching or bending of the bonds happening..?? (ideally, it should not...). 3) I want to calculate the power spectrum of the water (which can give more insights...). How can i do it in GROMACS..?? Any suggestions are highly appreciated. Thank you. --- With Best Regards, Dilip.H.N PhD Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 06/08/18, 1:42:08 PM -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
Re: [gmx-users] Distance between the atoms greater than Box length
Hi,
I have visualized the molecules in vmd and these two water molecules are
placed diagonally opposite in the box. So, in that case obviously, the
distance will be greater than the box length. And the two water molecules
are within the box only.
And yes, my box here is cubic.
Thank you.
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---
With Best Regards,
Dilip.H.N
PhD Student.
On Tue, Jun 5, 2018 at 7:09 AM, Mark Abraham
wrote:
> Hi,
>
> Only if the box is cubic.
>
> Mark
>
> On Tue, Jun 5, 2018 at 3:20 AM Quyen V. Vu wrote:
>
> > Hi Dillip,
> > As Mark suggest, If you want to calculate by your own code, you can put
> the
> > condition to check which is the nearest neighbour by comparing with box
> > length/2
> >
> >
> > On Mon, Jun 4, 2018, 19:42 Mark Abraham
> wrote:
> >
> > > Hi,
> > >
> > > You have a periodic cell, so in general the distance from A to the
> > nearest
> > > periodic image of B is across a cell boundary. Trjconv cannot produce a
> > > trajectory so that all pairs of A and B will have a non-periodic
> distance
> > > that is the minimum distance. Use a tool that already understands this,
> > > like
> > >
> > >
> > http://manual.gromacs.org/documentation/current/
> onlinehelp/gmx-distance.html
> > > or
> > >
> > http://manual.gromacs.org/documentation/current/
> onlinehelp/gmx-mindist.html
> > > .
> > >
> > > Mark
> > >
> > > On Mon, Jun 4, 2018, 14:01 Dilip.H.N
> wrote:
> > >
> > > > Hello all,
> > > > I have extracted the trajectory of my system containing all the water
> > > > molecules and my box length is 2.48 ~2.5 nm.
> > > > The command was:
> > > > gmx trjconv -f nptmd.xtc -s nptmd.tpr -pbc mol -o
> nptmdtrjwater500.gro
> > > -dt
> > > > 60 #i have 6 frames (30ns is the time and saved the
> > coordinates
> > > > for 0.5 ps )and i have extracted a total of 500 frames trajectory
> (-dt
> > 60
> > > > =>3/500).
> > > >
> > > > And i have written a code which calculates the inter-atomic distance
> > (in
> > > my
> > > > case it is inter oxygen distances). And when i calculate it (using
> the
> > > > distance formula ie.,
> > > > {sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the
> > oxygen
> > > > atom of say, 7SOL and 6SOL, the distance comes to 3.4520.
> > > >
> > > > Here are the coordinates for two water coordinates as
> representative...
> > > >
> > > > Generated by trjconv : Glycine-Water t= 0.0
> > > > xxx
> > > > .
> > > > .
> > > > .
> > > > 6SOL OW 13 2.405 0.185 1.774
> > > > 6SOLHW1 14 2.452 0.097 1.782
> > > > 6SOLHW2 15 2.466 0.259 1.804
> > > > 7SOL OW 16 0.016 2.177 0.277
> > > > 7SOLHW1 17 0.098 2.141 0.234
> > > > 7SOLHW2 18 -0.064 2.126 0.245
> > > > .
> > > > .
> > > > 2.49238 2.49238 2.49238
> > > >
> > > > How is this possible ie., 3.452 nm, which is greater than the box
> > length
> > > > (2.5 nm). How can the interatomic distance be greater than the box
> > > > length..??
> > > >
> > > > Any suggestions are appreciated.
> > > >
> > > > Thank you.
> > > >
> > > > [image: Mailtrack]
> > > > <
> > > >
> > >
> > https://mailtrack.io?utm_source=gmail_medium=signature_campaign=
> signaturevirality5&
> > > > >
> > > > Sender
> > > > notified by
> > > > Mailtrack
> > > > <
> > > >
> > >
> > https://mailtrack.io?utm_source=gmail_medium=signature_campaign=
> signaturevirality5&
> > > > >
> > > > 06/04/18,
> > > > 5:26:50 PM
> > > >
> > > > ---
> > > > With Best Regards,
> > > >
> > > > Dilip.H.N
> > > > PhD Student.
> > > >
> > > > On Mon, Jun 4, 2018 at 5:15 PM, Dilip.H.N >
> > > > wrote:
Re: [gmx-users] Distance between the atoms greater than Box length
Hello all,
I have extracted the trajectory of my system containing all the water
molecules and my box length is 2.48 ~2.5 nm.
The command was:
gmx trjconv -f nptmd.xtc -s nptmd.tpr -pbc mol -o nptmdtrjwater500.gro -dt
60 #i have 6 frames (30ns is the time and saved the coordinates
for 0.5 ps )and i have extracted a total of 500 frames trajectory (-dt 60
=>3/500).
And i have written a code which calculates the inter-atomic distance (in my
case it is inter oxygen distances). And when i calculate it (using the
distance formula ie.,
{sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the oxygen
atom of say, 7SOL and 6SOL, the distance comes to 3.4520.
Here are the coordinates for two water coordinates as representative...
Generated by trjconv : Glycine-Water t= 0.0
xxx
.
.
.
6SOL OW 13 2.405 0.185 1.774
6SOLHW1 14 2.452 0.097 1.782
6SOLHW2 15 2.466 0.259 1.804
7SOL OW 16 0.016 2.177 0.277
7SOLHW1 17 0.098 2.141 0.234
7SOLHW2 18 -0.064 2.126 0.245
.
.
2.49238 2.49238 2.49238
How is this possible ie., 3.452 nm, which is greater than the box length
(2.5 nm). How can the interatomic distance be greater than the box
length..??
Any suggestions are appreciated.
Thank you.
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---
With Best Regards,
Dilip.H.N
PhD Student.
On Mon, Jun 4, 2018 at 5:15 PM, Dilip.H.N wrote:
> Hello all,
> I have extracted the trajectory of my system containing all the water
> molecules and my box length is 2.48 ~2.5 nm.
>
> And i have written a code which calculates the inter-atomic distance (in
> my case it is inter oxygen distances). And when i calculate it (using the
> distance formula ie.,
> {sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the oxygen
> of say
> 6SOL OW 13 2.405 0.185 1.774
> 6SOLHW1 14 2.452 0.097 1.782
> 6SOLHW2 15 2.466 0.259 1.804
> 7SOL OW 16 0.016 2.177 0.277
> 7SOLHW1 17 0.098 2.141 0.234
> 7SOLHW2 18 -0.064 2.126 0.245
>
>
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
> [image: Mailtrack]
> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;>
> Sender
> notified by
> Mailtrack
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> 06/04/18,
> 5:15:08 PM
>
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[gmx-users] Distance between the atoms greater than Box length
Hello all,
I have extracted the trajectory of my system containing all the water
molecules and my box length is 2.48 ~2.5 nm.
And i have written a code which calculates the inter-atomic distance (in my
case it is inter oxygen distances). And when i calculate it (using the
distance formula ie.,
{sqrt [(x2-x1)**2+(y2-y1)**2+(z2-z1)**2]} the distance between the oxygen
of say
6SOL OW 13 2.405 0.185 1.774
6SOLHW1 14 2.452 0.097 1.782
6SOLHW2 15 2.466 0.259 1.804
7SOL OW 16 0.016 2.177 0.277
7SOLHW1 17 0.098 2.141 0.234
7SOLHW2 18 -0.064 2.126 0.245
---
With Best Regards,
Dilip.H.N
PhD Student.
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Re: [gmx-users] Regarding calculation of SDF
Hello, Hoping for a positive response... Thank you. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 05/31/18, 9:26:54 AM --- With Best Regards, Dilip.H.N PhD Student. On Mon, May 28, 2018 at 7:47 AM, Dilip.H.N wrote: > Hi, > I want to calculate the Spatial Distribution Function of say N-terminal > nitrogen atom and all the oxygen atoms of the water molecules. > So, i have created the index file in which i have the nitrogen atom and > all the oxygen atoms of water molecules. And here are my commands that i > gave inorder to calculate SDF: > gmx trjconv -s nptmd.tpr -f nptmd.xtc -n ndx_NOw.ndx -o abc.tng -ur > compact -pbc whole > gmx trjconv -s nptmd.tpr -f abc.tng -n ndx_NOw.ndx -o def.tng -fit > rot+trans > gmx spatial -s nptmd.tpr -n ndx_NOw.ndx -f def.tng -nab 10 > > I get the following: > Reading file nptmd.tpr, VERSION 2016.2 (single precision) > Select group to generate SDF: > Group 0 ( N) has 1 elements > Group 1 ( OW) has 511 elements > Select a group: 0 > Selected 0: 'N' > Select group to output coords (e.g. solute): > Group 0 ( N) has 1 elements > Group 1 ( OW) has 511 elements > Select a group: 1 > Selected 1: 'OW' > TNG library: Cannot uncompress data block. /home/dilip/Downloads/gromacs- > 2016.2/src/external/tng_io/src/lib/tng_io.c: 5298 > TNG library: Cannot uncompress data block. /home/dilip/Downloads/gromacs- > 2016.2/src/external/tng_io/src/lib/tng_io.c: 5298 > Last frame 6 time 3.000 > Back Off! I just backed up grid.cube to ./#grid.cube.1# > Counts per frame in all 27 cubes divided by 3.703704e-02 > Normalized data: average 1.00e+00, min 0.00e+00, max 2.70e+01 > > > and if i view the grid.cube file in vmd, i am unable to get a proper > SDF/it is wired when i give an isovalues and change its values... > > How can i solve this..?? > Any suggestions are highly appreciated. > > Thank you. > > --- > With Best Regards, > > Dilip.H.N > PhD Student. > [image: Mailtrack] > <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> > Sender > notified by > Mailtrack > <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> > 05/28/18, > 7:47:09 AM > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
[gmx-users] Regarding calculation of SDF
Hi, I want to calculate the Spatial Distribution Function of say N-terminal nitrogen atom and all the oxygen atoms of the water molecules. So, i have created the index file in which i have the nitrogen atom and all the oxygen atoms of water molecules. And here are my commands that i gave inorder to calculate SDF: gmx trjconv -s nptmd.tpr -f nptmd.xtc -n ndx_NOw.ndx -o abc.tng -ur compact -pbc whole gmx trjconv -s nptmd.tpr -f abc.tng -n ndx_NOw.ndx -o def.tng -fit rot+trans gmx spatial -s nptmd.tpr -n ndx_NOw.ndx -f def.tng -nab 10 I get the following: Reading file nptmd.tpr, VERSION 2016.2 (single precision) Select group to generate SDF: Group 0 ( N) has 1 elements Group 1 ( OW) has 511 elements Select a group: 0 Selected 0: 'N' Select group to output coords (e.g. solute): Group 0 ( N) has 1 elements Group 1 ( OW) has 511 elements Select a group: 1 Selected 1: 'OW' TNG library: Cannot uncompress data block. /home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c: 5298 TNG library: Cannot uncompress data block. /home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c: 5298 Last frame 6 time 3.000 Back Off! I just backed up grid.cube to ./#grid.cube.1# Counts per frame in all 27 cubes divided by 3.703704e-02 Normalized data: average 1.00e+00, min 0.00e+00, max 2.70e+01 and if i view the grid.cube file in vmd, i am unable to get a proper SDF/it is wired when i give an isovalues and change its values... How can i solve this..?? Any suggestions are highly appreciated. Thank you. --- With Best Regards, Dilip.H.N PhD Student. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;> 05/28/18, 7:47:09 AM -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
[gmx-users] Regarding getting good performance for mdrun
Hello all, My workstation has 1 node with total 24 cores, 48 logical cores. 1] I gave the command as: gmx mdrun -v -s abc.tpr -deffnm abc I got few messages as:- NOTE: Parallelization is limited by the small number of atoms, only starting 16 thread-MPI ranks. You can use the -nt and/or -ntmpi option to optimize the number of threads. Using 16 MPI threads Using 3 OpenMP threads per tMPI thread WARNING: This run will generate roughly 51484 Mb of data starting mdrun 'abc system' 100 steps, 1000.0 ps. step 00, remaining wall clock time: 0 s imb F 10% Writing final coordinates. step 100, remaining wall clock time: 0 s Average load imbalance: 11.0 % Part of the total run time spent waiting due to load imbalance: 1.7 % NOTE: 28 % of the run time was spent communicating energies, you might want to use the -gcom option of mdrun 2] and then if i give the command as: gmx mdrun -v -s abc.tpr -deffnm abc -ntmpi 6 -ntomp 8 I got: Using 6 MPI threads Using 8 OpenMP threads per tMPI thread step 36800, will finish Sat May 5 12:42:12 2018 imb F 6% So, My questions are:- a) Does the simulation run just with gmx mdrun, effect on the trajectories/output files b) "28 % of the run time was spent communicating" Has it affected the resulting output..?? c) what does this imb F means..?? and what is the significance of the percentage (say 1.7%) states/defines..?? c) Any other information regarding these are highly beneficial.. Thank you. --- With Best Regards, Dilip.H.N PhD Student. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid
Any suggestions as to how to write the script.? or on feeding the index file to trjconv manually...?? Thank you. [image: Mailtrack] <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality3;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality3;> --- With Best Regards, Dilip.H.N PhD Student. On Thu, Apr 12, 2018 at 1:48 PM, Joe Jordan <e.jjorda...@gmail.com> wrote: > Since gmx trjconv does not work with dynamic selections, you can either > feed the index file to trjconv and manually pick which frames to dump or > write a script that calls trjconv to dump the atoms you want for each > timestep you want. > > On Thu, Apr 12, 2018 at 10:04 AM, Dilip.H.N <cy16f01.di...@nitk.edu.in> > wrote: > > > The -on option too gives the output as in index format, which i don't > want. > > I want it in a .gro file and not as in an index file format.In gmx select > > options the output files are written in .xvg/.ndx.dat format only... > > i want the output to be written like the following:- > > > > frame t= 0.000 > > 1543 > > 1GLY N1 1.206 1.052 1.131 > > 1GLY H12 1.266 1.070 1.215 > > 1GLY H23 1.270 1.019 1.056 > > 1GLY H34 1.134 0.981 1.155 > > 1GLY CA5 1.158 1.191 1.103 > > 1GLYHA16 1.086 1.211 1.181 > > 1GLYHA27 1.127 1.205 1.001 > > 1GLY C8 1.276 1.289 1.123 > > 1GLYOT19 1.252 1.408 1.108 > > 1GLYOT2 10 1.392 1.257 1.149 > > 253SOL OW 764 1.085 0.998 0.837 > > 253SOLHW1 765 0.998 0.982 0.883 > > 253SOLHW2 766 1.109 0.919 0.781 > > 252SOL OW 761 0.848 1.089 0.990 > > 252SOLHW1 762 0.767 1.098 1.049 > > 252SOLHW2 763 0.881 1.180 0.965 > > . > > . > > frame t= 1.000 > > 1543 > > 1GLY N1 1.229 1.032 1.106 > > 1GLY H12 1.277 1.040 1.198 > > 1GLY H23 1.290 0.979 1.041 > > 1GLY H34 1.145 0.976 1.127 > > 1GLY CA5 1.198 1.175 1.059 > > 1GLYHA16 1.128 1.213 1.132 > > 1GLYHA27 1.175 1.175 0.953 > > 1GLY C8 1.309 1.273 1.082 > > 1GLYOT19 1.282 1.393 1.056 > > 1GLYOT2 10 1.417 1.237 1.137 > > 155SOL OW 470 1.005 1.448 1.113 > > 155SOLHW1 471 1.103 1.445 1.095 > > 155SOLHW2 472 0.957 1.477 1.030 > > 388SOL OW 1169 1.307 1.001 1.370 > > 388SOLHW1 1170 1.329 1.053 1.452 etc... > > > > Any suggestions are appreciated. > > > > Thank you. > > > > <https://mailtrack.io/> Sent with Mailtrack > > <https://mailtrack.io?utm_source=gmail_medium= > signature_campaign= > > signaturevirality&> > > > > --- > > With Best Regards, > > > > Dilip.H.N > > PhD Student. > > > > On Thu, Apr 12, 2018 at 1:12 PM, Joe Jordan <e.jjorda...@gmail.com> > wrote: > > > > > You need -on for gmx select to write out the index file. > > > > > > On Thu, Apr 12, 2018 at 8:48 AM, Dilip.H.N <cy16f01.di...@nitk.edu.in> > > > wrote: > > > > > > > I tried the following two ways ie., with gmx select and with gmx > > trjorder > > > > > > > > 1) when i give the command :- > > > > gmx trjorder -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -o order.gro > > > -nshell > > > > -r 0.35 > > > > > > > > i got an output file, it has all the water molecules (i have 511 > water > > > > molecules in my system) for each time frame but it has arranged > > according > > > > to the smallest distance to atoms in the reference group. (but i want > > > only > > > > those water molecules within 0.35nm of nitrogen of glycine molecule.) > > > > > > > > 2) in this command:- > > > > gmx select -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -oi -select > '"close > > > to > > > > name N" resname SOL and within 0.35 of group protein' > > > > > > > > i am getting an .dat file which has only the coordinates and the > format > > > on > > > > as in index file format. > > > > > > > > Actually, i wanted the format in which the gmx trjorder output gives > > (as
Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid
The -on option too gives the output as in index format, which i don't want. I want it in a .gro file and not as in an index file format.In gmx select options the output files are written in .xvg/.ndx.dat format only... i want the output to be written like the following:- frame t= 0.000 1543 1GLY N1 1.206 1.052 1.131 1GLY H12 1.266 1.070 1.215 1GLY H23 1.270 1.019 1.056 1GLY H34 1.134 0.981 1.155 1GLY CA5 1.158 1.191 1.103 1GLYHA16 1.086 1.211 1.181 1GLYHA27 1.127 1.205 1.001 1GLY C8 1.276 1.289 1.123 1GLYOT19 1.252 1.408 1.108 1GLYOT2 10 1.392 1.257 1.149 253SOL OW 764 1.085 0.998 0.837 253SOLHW1 765 0.998 0.982 0.883 253SOLHW2 766 1.109 0.919 0.781 252SOL OW 761 0.848 1.089 0.990 252SOLHW1 762 0.767 1.098 1.049 252SOLHW2 763 0.881 1.180 0.965 . . frame t= 1.000 1543 1GLY N1 1.229 1.032 1.106 1GLY H12 1.277 1.040 1.198 1GLY H23 1.290 0.979 1.041 1GLY H34 1.145 0.976 1.127 1GLY CA5 1.198 1.175 1.059 1GLYHA16 1.128 1.213 1.132 1GLYHA27 1.175 1.175 0.953 1GLY C8 1.309 1.273 1.082 1GLYOT19 1.282 1.393 1.056 1GLYOT2 10 1.417 1.237 1.137 155SOL OW 470 1.005 1.448 1.113 155SOLHW1 471 1.103 1.445 1.095 155SOLHW2 472 0.957 1.477 1.030 388SOL OW 1169 1.307 1.001 1.370 388SOLHW1 1170 1.329 1.053 1.452 etc... Any suggestions are appreciated. Thank you. <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality;> --- With Best Regards, Dilip.H.N PhD Student. On Thu, Apr 12, 2018 at 1:12 PM, Joe Jordan <e.jjorda...@gmail.com> wrote: > You need -on for gmx select to write out the index file. > > On Thu, Apr 12, 2018 at 8:48 AM, Dilip.H.N <cy16f01.di...@nitk.edu.in> > wrote: > > > I tried the following two ways ie., with gmx select and with gmx trjorder > > > > 1) when i give the command :- > > gmx trjorder -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -o order.gro > -nshell > > -r 0.35 > > > > i got an output file, it has all the water molecules (i have 511 water > > molecules in my system) for each time frame but it has arranged according > > to the smallest distance to atoms in the reference group. (but i want > only > > those water molecules within 0.35nm of nitrogen of glycine molecule.) > > > > 2) in this command:- > > gmx select -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -oi -select '"close > to > > name N" resname SOL and within 0.35 of group protein' > > > > i am getting an .dat file which has only the coordinates and the format > on > > as in index file format. > > > > Actually, i wanted the format in which the gmx trjorder output gives (as > in > > my case, order.gro), but i want only those water molecules which are > within > > 3.5 nm of the nitrogen atom of glycine molecule for each time frame. > > > > Any suggestions are appreciated. > > > > Thank you. > > > > > > <https://mailtrack.io/> Sent with Mailtrack > > <https://mailtrack.io?utm_source=gmail_medium= > signature_campaign= > > signaturevirality&> > > > > --- > > With Best Regards, > > > > Dilip.H.N > > PhD Student. > > > > On Wed, Apr 11, 2018 at 6:23 PM, Marc Hoemberger <hoemb...@brandeis.edu> > > wrote: > > > > > You can use either gmx trjorder with the nshell parameter (if it is as > > > simple as within Xnm of Y, use nshell parameter, see manual) or gmx > > select > > > (if you need some more complex selection). > > > > > > On Wed, Apr 11, 2018 at 3:54 AM, Dilip.H.N <cy16f01.di...@nitk.edu.in> > > > wrote: > > > > > > > Hello all, > > > > > > > > I want to get the water molecules which are at a certain distance > (say > > > all > > > > the water molecules which are within 0.35nm of the Nitrogen atom of > > > glycine > > > > molecule). How can i get this all the coordinates.? > > > > > > > > Any specific commands..?? > > > > > > > > > > > > Thank you. > > > > > > > > --- > > > > With Best Regards, > > > > > > > > Dilip.H.N > > > > PhD Student. > > > > <https
Re: [gmx-users] Regarding getting the coordinates within certain region of amino-acid
I tried the following two ways ie., with gmx select and with gmx trjorder 1) when i give the command :- gmx trjorder -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -o order.gro -nshell -r 0.35 i got an output file, it has all the water molecules (i have 511 water molecules in my system) for each time frame but it has arranged according to the smallest distance to atoms in the reference group. (but i want only those water molecules within 0.35nm of nitrogen of glycine molecule.) 2) in this command:- gmx select -f nptmd.xtc -s nptmd.tpr -n ndx_all.ndx -oi -select '"close to name N" resname SOL and within 0.35 of group protein' i am getting an .dat file which has only the coordinates and the format on as in index file format. Actually, i wanted the format in which the gmx trjorder output gives (as in my case, order.gro), but i want only those water molecules which are within 3.5 nm of the nitrogen atom of glycine molecule for each time frame. Any suggestions are appreciated. Thank you. <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality;> --- With Best Regards, Dilip.H.N PhD Student. On Wed, Apr 11, 2018 at 6:23 PM, Marc Hoemberger <hoemb...@brandeis.edu> wrote: > You can use either gmx trjorder with the nshell parameter (if it is as > simple as within Xnm of Y, use nshell parameter, see manual) or gmx select > (if you need some more complex selection). > > On Wed, Apr 11, 2018 at 3:54 AM, Dilip.H.N <cy16f01.di...@nitk.edu.in> > wrote: > > > Hello all, > > > > I want to get the water molecules which are at a certain distance (say > all > > the water molecules which are within 0.35nm of the Nitrogen atom of > glycine > > molecule). How can i get this all the coordinates.? > > > > Any specific commands..?? > > > > > > Thank you. > > > > --- > > With Best Regards, > > > > Dilip.H.N > > PhD Student. > > <https://mailtrack.io/> Sent with Mailtrack > > <https://mailtrack.io?utm_source=gmail_medium= > signature_campaign= > > signaturevirality&> > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read 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. > > > > > > -- > Marc Hoemberger > Ph.D. Candidate, Biochemistry and Biophysics, > Laboratory of Dorothee Kern > MS-009, 415 South St. > Brandeis University > Waltham, MA, 02453 > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read 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. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
[gmx-users] Regarding getting the coordinates within certain region of amino-acid
Hello all, I want to get the water molecules which are at a certain distance (say all the water molecules which are within 0.35nm of the Nitrogen atom of glycine molecule). How can i get this all the coordinates.? Any specific commands..?? Thank you. --- With Best Regards, Dilip.H.N PhD Student. <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality;> -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read 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.
