Re: [gmx-users] Regarding the charge of the atom in the .rtp file

Thank you for reply.. But how can i identify the molecule as methylamine (for example) since in the .rtp the molecule type is written as [MAM1] [ MAM1 ] [ atoms ] N1 NG321-0.990 0 C1 CG3AM2 -0.060 1 HN1 HGPAM20.390 2 HN2 HGPAM20.390 3 HC1 HGAAM20.090 4

Re: [gmx-users] GROMACS and SIMtoEXP

Thank you David, I realized my mistake and I need to be using number density when working with SIMtoEXP however, I was wondering if there is some script out there to easily convert my number density from gromacs to the compatible file format for SIMtoEXP. Regards, Sanim Rahman On Wed, Jun 21,

Re: [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

Victory! The -noparam did the trick :) Thanks a million. On Wed, Jun 21, 2017 at 11:43 AM, Justin Lemkul wrote: > > > On 6/21/17 11:39 AM, Jose Borreguero wrote: > >> Hi Justin, >> >> ​Thanks for your quick reply! ​ >> This means x2top is not finding >> ​ >> or using >> the

Re: [gmx-users] (no subject)

Hi, On Wed, Jun 21, 2017 at 4:32 PM Shivangi Agarwal < shivangi.agarwal...@gmail.com> wrote: > Hi > But it is broken. .. > Nope, it's just in one of the infinite number of equivalent representations of the same thing ;-) mdrun doesn't know that you want it to write a file where your protein and

Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

Hi, On Wed, Jun 21, 2017 at 6:49 PM Diez Fernandez, Amanda < amanda.die...@imperial.ac.uk> wrote: > Hi Justin, > Thank you for your reply. > > Here are the links to the images of: > -the output coordinates > -and last frame of trajectory. > > Output coordinates which look wrong: >

Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

Hi Justin, Thank you for your reply. Here are the links to the images of: -the output coordinates -and last frame of trajectory. Output coordinates which look wrong: http://i1036.photobucket.com/albums/a443/amanda222lld/output_coordinates_zp stuqkgjd2.png Last frame from trajectory which looks

Re: [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

On 6/21/17 11:39 AM, Jose Borreguero wrote: Hi Justin, ​Thanks for your quick reply! ​ This means x2top is not finding ​ or using the right force constant value, right? ​ I ​ did add the bond info into file ffbonded.itp ​of the oplsa.ff/ directory ​ (https://goo.gl/z5UMot) . I also

Re: [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

Hi Justin, ​Thanks for your quick reply! ​ This means x2top is not finding ​ or using the right force constant value, right? ​ I ​ did add the bond info into file ffbonded.itp ​of the oplsa.ff/ directory ​ (https://goo.gl/z5UMot) . I also included the types in file atomtypes.atp ​ and the non

Re: [gmx-users] Genion

Indeed, thanks: I did it manually. Will try updating the top with genion, Sergio Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

On 6/21/17 10:55 AM, gozde ergin wrote: However in the paper they have mentioned that they increased the sigma for amino nitrogen–carboxylate oxygen interactions by 0.13Angstrom relative to the original value. So I assume there should be original value? However you mentioned that there is

Re: [gmx-users] Genion

Hi Justin, the sequence was: gmx editconf gmx solvate gmx grompp -f em -c dna_solvated.gro -p topol_solvated -o dna_solv.tpr gmx genion -s dna_solv.tpr -o dna_solv_NaCl.gro -conc 0.15 -neutral -pname NA -nname CL then: gmx grompp -f em.mdp -c dna_solv_NaCl.gro -p

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

However in the paper they have mentioned that they increased the sigma for amino nitrogen–carboxylate oxygen interactions by 0.13Angstrom relative to the original value. So I assume there should be original value? However you mentioned that there is no pair-specific LJ interaction in OPLSAA.

Re: [gmx-users] Genion

On 6/21/17 10:45 AM, Sergio Manzetti wrote: Hi Justin, the sequence was: gmx editconf gmx solvate gmx grompp -f em -c dna_solvated.gro -p topol_solvated -o dna_solv.tpr gmx genion -s dna_solv.tpr -o dna_solv_NaCl.gro -conc 0.15 -neutral -pname NA -nname CL then: gmx grompp -f

Re: [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

On 6/21/17 10:47 AM, Jose Borreguero wrote: Dear Gromacs users, I created the .top file for a small silica crystal that contains only two types of atoms, silicon (type SIO) and oxygen (type OSI). The bond potential is: [ bondtypes ] ; ij func b0 kb SIO OSI 1 ​ ​

[gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

Dear Gromacs users, I created the .top file for a small silica crystal that contains only two types of atoms, silicon (type SIO) and oxygen (type OSI). The bond potential is: [ bondtypes ] ; ij func b0 kb SIO OSI 1 ​ ​ 0.15783 ​ ​ 251040 After running gmx x2top,

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

On 6/21/17 10:39 AM, gozde ergin wrote: Hi MArk, Thanks for the respond. I understood that point however I still do not get which sigma to change. I the paper JCTC 2017, Miller et. al. they have mentioned that they increase the for nitrogen–carboxylate oxygen interactions in OPLSAA. However

Re: [gmx-users] Genion

On 6/21/17 10:30 AM, Sergio Manzetti wrote: Hello, genion worked, and grompp was used to run the output conf from genion. Mdrun minimized all OK, however, mdrun produced a counfout.gro file that no longer contains the Na Cl ions added to the system. When setting up the simulation, the input

Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

On 6/21/17 7:11 AM, Diez Fernandez, Amanda wrote: Hi all, I am running a simulation and I find that the output coordinates of the simulation stored in “final_coordinates.gro” are distinctively different to any of the frames from “trajectory.gro” which I obtain from : trjconv –s file.tpr –f

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

Hi MArk, Thanks for the respond. I understood that point however I still do not get which sigma to change. I the paper JCTC 2017, Miller et. al. they have mentioned that they increase the for nitrogen–carboxylate oxygen interactions in OPLSAA. However there are two sigma in

[gmx-users] Genion

Hello, genion worked, and grompp was used to run the output conf from genion. Mdrun minimized all OK, however, mdrun produced a counfout.gro file that no longer contains the Na Cl ions added to the system. When setting up the simulation, the input confout.gro has no Na Cl ions, and the

Re: [gmx-users] (no subject)

Hi But it is broken. .. strand with proline with three odr residues has been broken and visible... i have Checked in vmd and pymol On 21 Jun 2017 17:16, "Mark Abraham" wrote: > Hi, > > On Wed, Jun 21, 2017 at 1:21 PM Shivangi Agarwal < > shivangi.agarwal...@gmail.com>

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

Hi, Different force fields work differently and thus are implemented differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma is a property of the atomtype Mark On Wed, Jun 21, 2017 at 4:16 PM gozde ergin wrote: > Dear users, > > I am trying to change

[gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

Dear users, I am trying to change the sigma value of amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS. However I have difficulties to understand which parameter i should change in ffnonbonded.itp file? I am looking something like [ nonbond_params ] section however it is not

Re: [gmx-users] Error running GMX 5.14

Thanks, this worked. Sergio Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [

Re: [gmx-users] Slow MDRUN performance

Hi, OK. The build system will choose these defaults correctly for you if you just leave things alone ;-) Mark On Wed, Jun 21, 2017 at 1:17 PM Syed Azeem wrote: > > > > Hi, > > > > On Wed, Jun 21, 2017 at 12:47 PM Syed Azeem > > >

Re: [gmx-users] (no subject)

Hi, On Wed, Jun 21, 2017 at 1:21 PM Shivangi Agarwal < shivangi.agarwal...@gmail.com> wrote: > Hello to all gmx users > > I am performing protein ligand complex MD simulation but my protein > structure has been broken during energy minimization process. > It's not broken, but rather in an

[gmx-users] (no subject)

Hello to all gmx users I am performing protein ligand complex MD simulation but my protein structure has been broken during energy minimization process. What may be the suitable reason? How I can solve this? Your support is highly appreciated -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Slow MDRUN performance

> > Hi, > > On Wed, Jun 21, 2017 at 12:47 PM Syed Azeem > wrote: > >> Hi all, >> >> I installed gromacs 5.1.2 on a new machine. >> Config: Intel Core i5 6500 3.20 GHz Quad Core Skylake with 8 GB DDR4. >> >> Then I started a NVT simulation for 500ps with ~25 atom

[gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

Hi all, I am running a simulation and I find that the output coordinates of the simulation stored in “final_coordinates.gro” are distinctively different to any of the frames from “trajectory.gro” which I obtain from : trjconv –s file.tpr –f trajectory.xtc –o trajectory.gro When I visualise

Re: [gmx-users] Protein-ligand binding Cut-offs

Hi, You aren't getting output because you aren't actually making a selection - see "gmx help select" and its suggestions for where to look for the rest of the documentation and explained examples. Mark On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash wrote: > I'm not

Re: [gmx-users] Regarding the charge of the atom in the .rtp file

Hi, On Wed, Jun 21, 2017 at 11:59 AM Dilip H N wrote: > Hello all. > 1] I want to knw how the charges are designated/assigned for the each atoms > in molecule in the .rtp file. ie., as example for methylamine in CHARMM > FF:- > > [ MAM1 ] > [ atoms ] > N1 NG321

Re: [gmx-users] Slow MDRUN performance

Hi, On Wed, Jun 21, 2017 at 12:47 PM Syed Azeem wrote: > Hi all, > > I installed gromacs 5.1.2 on a new machine. > Config: Intel Core i5 6500 3.20 GHz Quad Core Skylake with 8 GB DDR4. > > Then I started a NVT simulation for 500ps with ~25 atom system. >

[gmx-users] Slow MDRUN performance

Hi all, I installed gromacs 5.1.2 on a new machine. Config: Intel Core i5 6500 3.20 GHz Quad Core Skylake with 8 GB DDR4. Then I started a NVT simulation for 500ps with ~25 atom system. Surprisingly, the estimated time was 4 days and 3 hours. There was a note stating consider rebuilding gmx

Re: [gmx-users] Protein-ligand binding Cut-offs

I'm not sure if the command I entered (shown below) is correct. No output was given. I'm unclear as to how this command will enable me to isolate the glycine molecules within 4A of the protein molecule? gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos whole_mol_com -seltype

[gmx-users] Regarding the charge of the atom in the .rtp file

Hello all. 1] I want to knw how the charges are designated/assigned for the each atoms in molecule in the .rtp file. ie., as example for methylamine in CHARMM FF:- [ MAM1 ] [ atoms ] N1 NG321-0.990 0 C1 CG3AM2 -0.060 1 HN1 HGPAM20.390 2 HN2 HGPAM20.390 3 HC1

Re: [gmx-users] Computing work from pulling simulations

Have you compared the results of your calculation using the forces at different intervals? e.g. every 1, 10, 50, 100 steps ? As long as you use a not-so-large interval the result should be the same within statistical error. Cheers, Leandro On Mon, Jun 19, 2017 at 7:19 PM, Lutz Maibaum

Re: [gmx-users] a problem about ewald geometry=3dc

If you can not make sure that the atoms stay inside the slab you should use 3D electrostatics. The 3DC method an approximation, which gives the same results as true 2D electrostatics only for a thin slab. When atoms leave the slab the potentials and forces comparing 2D and 3DC are not

Re: [gmx-users] Difference between Err. Est. And RMSD

Thanks João for the answer. Thanks Justin for sharing reference. Justin, What will be your brief suggestion for the question, " which one among Err.Est or RMSD should I use to show error bars in the plot. " If I have to report box-X and box-Y in the publication. Thank you. > On 20-Jun-2017,

Re: [gmx-users] GROMACS and SIMtoEXP

On 20/06/17 23:16, Sanim Rahman wrote: Hello Everyone, I am interested in using the SIMtoEXP program to directly compare my simulation results to experimental values. The program only can process electron density profiles written as .dat and .sim files. Is anyone aware of scripts or GROMACS