[gmx-users] Re: energy conservation: shift vs shifted user potential

Hello all, can someone give me a hint, please? Do you need more information? Has anyone had a similar problem. I really need to figure that out, because I will simulate other systems which can be run only with user tables. Anja - - Original Message - - Original Message -

[gmx-users] Pulling - ligand outside the box

Dear Gmx Users, I pulled my ligand away from the protein and I found out that after getting rid of PBC (trjconv -pbc whole) my ligand goes outside the box? Is it fine or should I increase my box as I want to run umbrella sampling? Thanks, Steven -- gmx-users mailing list

Re: [gmx-users] Pulling - ligand outside the box

On 8/06/2012 8:35 PM, Steven Neumann wrote: Dear Gmx Users, I pulled my ligand away from the protein and I found out that after getting rid of PBC (trjconv -pbc whole) There is no magic way to get rid of PBC, and -pbc whole is certainly not it. Read trjconv -h and see

[gmx-users] eneconv with -dt flag

Hi all, I have encountered a problem using eneconv with -dt flag. I have several energy files. Firstly, I concatenated them using the following. eneconv -f first.edr second.edr -settime -o total.edr But, total.edr is so large. To reduce the size of file, I used the below command:

[gmx-users] QM/MM Calculation with Orca

Dear GROMACS Users, I am using Gromacs with ORCA for a qm calculation, but I can only use 1 processor for mdrun. If I place the line !PAL4 in the topol.ORCAINFO and run mdrun -nt 1, it works, and ORCA parallelizes correctly for 4 processors, although mdrun only runs one thread. If I place the

[gmx-users] md.log i/o error in futil.c +459

Good afternoon! I'm getting the following error message from mdrun, and despite trying, I can't seem to find the file futil.c in which the error is supposed to be taking place. Can anyone help me out, please? Thanks, and have a good weekend! Inon.

Re: [gmx-users] md.log i/o error in futil.c +459

On 8/06/2012 11:05 PM, Inon Sharony wrote: Good afternoon! I'm getting the following error message from mdrun, and despite trying, I can't seem to find the file futil.c in which the error is supposed to be taking place. Can anyone help me out, please? It's the source file of GROMACS that

Re: [gmx-users] eneconv with -dt flag

On 8/06/2012 10:40 PM, Turgay Cakmak wrote: Hi all, I have encountered a problem using eneconv with -dt flag. I have several energy files. Firstly, I concatenated them using the following. eneconv-f first.edr second.edr -settime -o total.edr But, total.edr is so large. To reduce

Re: [gmx-users] Re: energy conservation: shift vs shifted user potential

On 8/06/2012 5:59 PM, Anja Kuhnhold wrote: Hello all, can someone give me a hint, please? Do you need more information? Has anyone had a similar problem. I really need to figure that out, because I will simulate other systems which can be run only with user tables. Anja - - Original

[gmx-users] 4. QM/MM Calculation with Orca (Minos Matsoukas)

YOucan only use one thread in mdrun, but more than one in ORCA. Try to estimate the ratio of computation time spent between the QM and MM calculation to get an idea of why we never bothered to parallellize the MM part. Hope this helps, Gerrit 4. QM/MM Calculation with Orca (Minos

Re: [gmx-users] qmmm and real-life meaning of null

Hi, INdeed, you would still need a LJ term for the QM atoms, in order to interact with the MM atoms. Only if the radius around your special atom were larger than the LJ cut-off could you safely ignore the LJ paramter. gerrit Message: 3 Date: Thu, 07 Jun 2012 19:47:02 -0400 From: Justin

[gmx-users] Furthest distance between 2 atoms

Hi everybody, I am trying to find an easy way to calculate the furthest distance between the atoms of two groups in a system. I know that g_dist can give me all the distances I want, but I would have to run g_dist for each possible atom pair (which is not a fast or a straightforward process). I

Re: [gmx-users] eneconv with -dt flag

Thanks Mark. I want to calculate Coulomb and Lennard-Jones energies using total_dt100.edr . But, I am not sure I can get the correct energies? Turgay 2012/6/8 Mark Abraham mark.abra...@anu.edu.au On 8/06/2012 10:40 PM, Turgay Cakmak wrote: Hi all, I have encountered a problem using

Re: [gmx-users] eneconv with -dt flag

On 8/06/2012 11:51 PM, Turgay Cakmak wrote: Thanks Mark. I want to calculate Coulomb and Lennard-Jones energies using total_dt100.edr . But, I am not sure I can get the correct energies? Neither am I. Only you know the history of these .edr files. Mark Turgay 2012/6/8 Mark Abraham

[gmx-users] parameters for bond types for GROMOS force field.

Dear Gromacs Users! I'm looking for description of the parameters of bonds terms ( termed as the gb_# in the topology.top file) . Could you tell me where I could find such descriptions for all possible bond types ? thanks, James -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Furthest distance between 2 atoms

On 8/06/2012 11:49 PM, Catarina Santos wrote: Hi everybody, I am trying to find an easy way to calculate the furthest distance between the atoms of two groups in a system. I know that g_dist can give me all the distances I want, but I would have to run g_dist for each possible atom pair

Re: [gmx-users] parameters for bond types for GROMOS force field.

On 9/06/2012 12:00 AM, James Starlight wrote: Dear Gromacs Users! I'm looking for description of the parameters of bonds terms ( termed as the gb_# in the topology.top file) . Could you tell me where I could find such descriptions for all possible bond types ? See manual for literature

[gmx-users] Total energy of a group of atoms

Dear All, I'm planning to build a qm/mm interface using ase package (https://wiki.fysik.dtu.dk/ase/ ). Question: Is it possible to divide the system in two (or more) groups say group1: qm group2 : mm and get the total energy assoaciated to each of the groups? (both bonded and non-bonded

Re: [gmx-users] qmmm and real-life meaning of null lennard-jones parameters

The system in you topology must be complete even for QMMM, so you'll need FF parameters also for the QM part. Partition models for QM/MM work with the following energy decomposition: E(total) = E(QM_system) + E(MM_system) + E(QM-MM interaction) E(QM_system) and E(MM_system) are easy to define

[gmx-users] Electrostatic interaction energy

Hi all, I have 2 questions related to the electrostatic energy of the system.. 1) Is *total electrostatic energy* equal to *Coulomb-(SR)* + *Coul.-recip*. OR *Coulomb-14* + *Coulomb-(SR)* + *Coul.-recip*. I am so confused. I specified in my .mdp file; coulombtype = PME rvdw = 1.0 rlist = 1.0

Re: [gmx-users] Electrostatic interaction energy

On 6/8/12 11:04 AM, Turgay Cakmak wrote: Hi all, I have 2 questions related to the electrostatic energy of the system.. 1) Is *total electrostatic energy* equal to *Coulomb-(SR)* + *Coul.-recip*. OR *Coulomb-14* + *Coulomb-(SR)* + *Coul.-recip*. I am so confused. The total electrostatic

[gmx-users] Re: Re: energy conservation: shift vs shifted user potential

Ok, I try to explain it again :) I know the format of the user tables (x, f(x), -f'(x), g(x), -g'(x), h(x), -h'(x); f is coulomb, g dispersion, h repulsion). For testing the simple cut-off version, my table looks like the example in the installation. So I run a simulation with vdwtype=cut-off and

[gmx-users] vsite as interaction site for COM of benzene

Hi all, i have a more conceptional question, for using vsites as interaction-centers for coarse-grained particles: First the simple case: I want to simulate one benzene molecule (atomistic - aa) in coarse-grained (cg-) benzene (each benzene molecule as a single particle). For the cg-cg

Re: [gmx-users] parameters for bond types for GROMOS force field.

I've found that information in ffbonded.itp but I'm not sure about exactly meaning of some types. E.g I'm looking for bond type for simple double bond between C=C as well as C=N ( here both atoms in 5-m ring) atoms pairs. Should I use for the first one #define gb_15 0.1390 8.6600e+06 ;

Re: [gmx-users] parameters for bond types for GROMOS force field.

On 6/8/12 1:22 PM, James Starlight wrote: I've found that information in ffbonded.itp but I'm not sure about exactly meaning of some types. E.g I'm looking for bond type for simple double bond between C=C as well as C=N ( here both atoms in 5-m ring) atoms pairs. Should I use for the first

Re: [gmx-users] parameters for bond types for GROMOS force field.

Justin, Does the gb_10 suitable for both bonds that I want to parametrise ? As I've told previously I need to parametrise two different bonds 1) is the C=C bond wich are not in the ring. This is just double bound in linnear sequence -C=C-. 2) is the C=N- double bond where both atoms in the 5-m

Re: [gmx-users] parameters for bond types for GROMOS force field.

On 6/8/12 2:01 PM, James Starlight wrote: Justin, Does the gb_10 suitable for both bonds that I want to parametrise ? As I've told previously I need to parametrise two different bonds 1) is the C=C bond wich are not in the ring. This is just double bound in linnear sequence -C=C-. 2) is

Re: [gmx-users] parameters for bond types for GROMOS force field.

Justin, thanks alot. I'll try to use gb_10 ( for C=N) as well as gb_16 ( for C=C) for parametrisation in my task. James 2012/6/8 Justin A. Lemkul jalem...@vt.edu On 6/8/12 2:01 PM, James Starlight wrote: Justin, Does the gb_10 suitable for both bonds that I want to parametrise ? As

[gmx-users] Energy Minimization - not getting correct lipid area

Hi, I am working through the KALP-15 tutorial and having difficulties getting the correct area per lipid (~71 A^2). I first scaled the lipid by a factor of 4 (perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat) then did energy minimization (mdrun -v -deffnm em) and then

Re: [gmx-users] Energy Minimization - not getting correct lipid area

On 6/8/12 3:15 PM, Hicks, Erica wrote: Hi, I am working through the KALP-15 tutorial and having difficulties getting the correct area per lipid (~71 A^2). I first scaled the lipid by a factor of 4 (perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat) then did energy

[gmx-users] CECAM ScalaLife Workshop, Oct 03 - Oct 05, 2012

Dear GROMACS Users, GROMACS is one of the applications participating in the ScalaLife EU project (www.scalalife.eu). ScalaLife is organising a CECAM workshop on High Performance Computing in Computational Chemistry and Molecular Biology: Challenges and Solutions provided by ScalaLife

Re: [gmx-users] Re: Energy Minimization - not getting correct lipid area

On 6/8/12 4:57 PM, Erica Hicks wrote: It was after just one iteration. The number of lipids removed after scaling the lipids by a factor of 4 was two. I am not sure how to update this as the [molecules] directive in the topology.top shows only the number of moles, i.e. 1. The number shown

[gmx-users] floating point exception in .xtc file

Dear Users: I have a 500 ns trajectory of 65 GB that gives a floating point exception when I run it through gmxcheck or trjcat (generated and analyzed with gromacs 4.5.5). Has anybody encountered this? I ran mdrun with -append so this is the xtc resulting from months of simulation of a

[gmx-users] RE: Energy Minimization - not getting correct lipid area

Hi, I went back and found that a possible error could be that the coordinate file was not updated correctly. After concatenated the Kalp_newbox.gro and dppc128_whole.gro, it said to update the coordinate file with the correct number of atoms. This should be the topology.top, right? But when I

Re: [gmx-users] RE: Energy Minimization - not getting correct lipid area

On 6/8/12 5:32 PM, Erica Hicks wrote: Hi, I went back and found that a possible error could be that the coordinate file was not updated correctly. After concatenated the Kalp_newbox.gro and dppc128_whole.gro, it said to update the coordinate file with the correct number of atoms. This

[gmx-users] RE: Energy Minimization - not getting correct lipid area

Hi, Everything should be updated correctly. I added in the DPPC 128 underneath the protein in [molecules] but I still get the same results. What do you mean by Further manual modifications are necessary based on how many lipids InflateGRO removes? After I generated the new position restrain

Re: [gmx-users] RE: Energy Minimization - not getting correct lipid area

On 6/8/12 6:18 PM, Erica Hicks wrote: Hi, Everything should be updated correctly. I added in the DPPC 128 underneath the protein in [molecules] but I still get the same results. What do you mean by Further manual modifications are necessary based on how many lipids InflateGRO removes? After

[gmx-users] RE: Energy Minimization - not getting correct lipid area

Hi, bash-3.2$ perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Reading. Scaling lipids There are 128 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids in the lower leaflet Centering protein Checking

Re: [gmx-users] vsite as interaction site for COM of benzene

Dear Thomas, Whilst in principle a constraint should do what you are asking, you might be better off using multiple vsites to solve the problem so that there is an algebraic as apposed to numerical mapping of the forces. My immediate thought is to use two type 3 (or if necessary type 3fd) virtual

Re: [gmx-users] RE: Energy Minimization - not getting correct lipid area

On 6/8/12 6:33 PM, Erica Hicks wrote: Hi, bash-3.2$ perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Reading. Scaling lipids There are 128 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids in the lower

[gmx-users] RE: Energy Minimization - not getting correct lipid area

How would I know what coordinate file to use? I have been following the tutorial word for word. However, I did not get the confout.gro file that I should have gotten after the minimization (mdrun -v -deffnm em) so I have been using em.gro. Would this be a problem?

Re: [gmx-users] RE: Energy Minimization - not getting correct lipid area

On 6/8/12 6:54 PM, Erica Hicks wrote: How would I know what coordinate file to use? I have been following the tutorial word for word. However, I did not get the confout.gro file that I should have gotten after the minimization (mdrun -v -deffnm em) so I have been using em.gro. Would this be a

[gmx-users] vsite as interaction site for COM of benzene

Dear Richard, thanks for the idea, i will try this. Relating to your side note: I perform pulling simulations of a calixarene-catenane dimer (both together 600 atoms) and i mesitylene as a solvent. To access longer time-scales I wanted to coarse-grain the solvent only. My supervisor said that

Re: [gmx-users] Re: Re: energy conservation: shift vs shifted user potential

On 9/06/2012 2:05 AM, Anja Kuhnhold wrote: Ok, I try to explain it again :) I know the format of the user tables (x, f(x), -f'(x), g(x), -g'(x), h(x), -h'(x); f is coulomb, g dispersion, h repulsion). For testing the simple cut-off version, my table looks like the example in the installation.

Re: [gmx-users] floating point exception in .xtc file

On 9/06/2012 7:27 AM, Christopher Neale wrote: Dear Users: I have a 500 ns trajectory of 65 GB that gives a floating point exception when I run it through gmxcheck or trjcat (generated and analyzed with gromacs 4.5.5). Has anybody encountered this? I ran mdrun with -append so this is the xtc

Re: [gmx-users] floating point exception in .xtc file

Hi Christopher, you can try to use the program gmx_rescue, by Marc Baaden to recovery your trajectory. Below there is the adderess: http://baaden.free.fr/soft/compchem.html Francesco 2012/6/9 Mark Abraham mark.abra...@anu.edu.au On 9/06/2012 7:27 AM, Christopher Neale wrote: Dear Users: