Re: [gmx-users] Question about "gmx traj" command

, Oct 16, 2017 at 10:38 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/16/17 9:36 AM, Chang Woon Jang wrote: > >> Dear Gromacs Users, >> >> I have a question about the gmx traj in order to calculate the force >> components. >>

[gmx-users] Question about "gmx traj" command

Dear Gromacs Users, I have a question about the gmx traj in order to calculate the force components. I used the following command. > gmx traj -f topol_new.trr -s topol_new.tpr -af force_all_z_l9.xvg -z yes It produced "force_all_z_l9.xvg" file. In the file, there are four columns. The first

Re: [gmx-users] Three molecules in single topol.top file

Dear Mark Abraham, I am a little confused about the meaning of "you have not taught grompp how to handle" (especially *taught*) because I have topology file, conf.gro, nonbonded and bonded force fields, grompp.mdp, index file. Do I need to do something else in order to specify the

Re: [gmx-users] Three molecules in single topol.top file

Dear Nikhil Maroli, I think that the error comes from the incorrect format of topology file. Therefore, I would like to create correct topology file for three molecules. The system I used is a customized coarse-grained system to which I mapped the atomistic system. Therefore, I need to modify

Re: [gmx-users] Three molecules in single topol.top file

Dear Sako Mirzaie, Thank you for your response. Do you mean that there is no way to include topologies in a single topol.top, and I need to separate them into three pieces of itp files? Best regards, Changwoon Jang On Wed, Aug 31, 2016 at 11:57 AM, SAKO MIRZAIE

Re: [gmx-users] Three molecules in single topol.top file

Dear Nikhil Maroli, Thank you for your link. However, I think that the link is just the example for a single type of molecule. My has three different types of molecules combined into a single topology file (topol.top). In the previous, I have three (TDM, J230, JMT) moleculetypes. I have

[gmx-users] Three molecules in single topol.top file

Dear Gromacs Users, I have a single topol.top file containing three molecules. Does this format is correct because the simulation keeps failing? Thank you. [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 0.0

Re: [gmx-users] I have questions for tabulated bonded potentials

Dear Justin Lemkul, I got it. Thank you very much for your help. Best regards, Changwoon Jang On Tue, Aug 30, 2016 at 8:40 PM, Chang Woon Jang <changwoonj...@gmail.com> wrote: > Dear Justin, > > >Do you mean "Order of parameters"? If I would like to specif

Re: [gmx-users] I have questions for tabulated bonded potentials

Dear Justin, Do you mean "Order of parameters"? If I would like to specify for table_b1.xvg, I need to set 1 after 8. If I would like to specifiy for table_b2.xvg, I need to set 2 after 8. Am I right? Best regards, Changwoon Jang On Tue, Aug 30, 2016 at 8:35 PM, Chang Woon Jang &

Re: [gmx-users] I have questions for tabulated bonded potentials

ith 8 or 9, but there is no explanation for distingushing several tables to specify different bonded interactions. Thank you. Best regards, Changwoon Jang On Tue, Aug 30, 2016 at 8:19 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/30/16 8:11 PM, Chang Woon Jang wrote

Re: [gmx-users] I have questions for tabulated bonded potentials

files in topol.top? Thank you. Best regards, Changwoon Jang On Tue, Aug 30, 2016 at 4:31 PM, Chang Woon Jang <changwoonj...@gmail.com> wrote: > Dear Gromacs Users, > > I have several bond, angle, dihedral potentials named table_b1.xvg, > table_b2.xvg, table_b3.xvg ...tabl

[gmx-users] I have questions for tabulated bonded potentials

Dear Gromacs Users, I have several bond, angle, dihedral potentials named table_b1.xvg, table_b2.xvg, table_b3.xvg ...table_a1.xvg, table_a2.xvg ... table_d1.xvg, table_d2.xvg, table_d3.xvg, table_d4.xvg. In my system, there are 6 types of beads (A, B, C, D, E, F). How can I assign each

Re: [gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

/30/16 11:52 AM, Chang Woon Jang wrote: > >> Dear Justin Lemkul, >> >> Thank you for your answers. The following is the error message after I >> run " gmx mdrun -s topol.tpr -c confgout.gro -o traj.trr -x traj.xtc -rdd >> 2.5". >> >> >>

Re: [gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

ion/Errors --- Best regards, Changwoon Jang On Tue, Aug 30, 2016 at 11:30 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/30/16 10:41 AM, Chang Woon Jang wrote: > >> Dear Justin Lemkul, >> Thank you for your response. Yes, I use coarse-grained system >>

Re: [gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

at 8:37 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/29/16 6:02 PM, Chang Woon Jang wrote: > >> Dear Gromacs Users, >> >> >> I have a Fatal error as follow. The error says -rdd option or -ddcheck. >> How >> can I properly use

[gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

Dear Gromacs Users, I have a Fatal error as follow. The error says -rdd option or -ddcheck. How can I properly use these options? Is the following command the proper use of these options? > gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc -rdd 1.5 -ddcheck Thank you. 1 of the

Re: [gmx-users] output file format under pbc

he -pbc mol option of trjconv is probably > what you're searching for. > > Marlon Sidore > > > PhD Student > Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM) > CNRS - UMR7255 > 31, Chemin Joseph Aiguier > 13402 cedex 20 Marseille > France > >

Re: [gmx-users] output file format under pbc

Dear Justin Lemkul, Thank you. I am going to try it. I tried to understand trjconv via the manual. Best regards, Changwoon Jang -- 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

Re: [gmx-users] output file format under pbc

Dear Gromacs Users, I would like to describe the situation. An initial molecule in the periodic boundary condition is located near the right side of box. The box is big, thus needs to be adjusted and equilibrated under NPT. The box should be shrinked after few ns seconds. The molecule near the

Re: [gmx-users] output file format under pbc

Dear Sir, Attached are figures here. Thank you. Best regards, Changwoon Jang -- 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

Re: [gmx-users] output file format under pbc

Dear Gromacs Users, Sorry for the misspelling of "Grimaces Users" due to automatic predictive text function. I am waiting for the answer. Thank you. Best regards, Changwoon Jang -- Gromacs Users mailing list * Please search the archive at

[gmx-users] output file format under pbc

Dear Grimaces Users, When I run a simulation with NPT under periodic boundary condition, the output file (confout.gro) is obtained with shrinked box due to the external pressure. Because of the periodic boundary condition, some molecules might be cross the boundary appearing the other side of

[gmx-users] decomposition error: -rdd and -dds do not influence the number of ranks

Dear MarK Abraham and Grimaces Users, Due to the limitation of Message body. I would like to open another ticket. I have tried DD control options such as -rdd and -dds but still the same error comes out. The key is to change the number of ranks. These DD control options do not influence

Re: [gmx-users] decomposition error

html > > Mark > > On Sat, 23 Jul 2016 03:34 Chang Woon Jang <changwoonj...@gmail.com> wrote: > > > Dear Mark Abraham, > > > > I am a little confused about the number of ranks. How can I choose > the > > number of ranks? Is this mdrun o

Re: [gmx-users] decomposition error

ards, Changwoon Jang On Fri, Jul 22, 2016 at 9:16 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Sat, 23 Jul 2016 03:05 Chang Woon Jang <changwoonj...@gmail.com> wrote: > > > Dear Mark Abraham, > > > >Thank you for the de

Re: [gmx-users] decomposition error

r 12 can give > you more joy > > Mark > > On Sat, 23 Jul 2016 01:42 Chang Woon Jang <changwoonj...@gmail.com> wrote: > > > Dear Justin Lemkul, > > > >I have looked at the log file as below. > > > > Initializing Domain Decomposition on 16

Re: [gmx-users] decomposition error

The maximum allowed number of cells is: X 3 Y 3 Z 3 Does this mean that I need to use "-dds 1.25" mdrun option? Thank you. Best regards, Changwoon Jang On Fri, Jul 22, 2016 at 7:07 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/22/16 7:03 PM, Chang Woon Jan

Re: [gmx-users] decomposition error

] ; Compound#mols DGA 200 J400 100 On Fri, Jul 22, 2016 at 6:59 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/22/16 6:50 PM, Chang Woon Jang wrote: > >> Dear Grimaces Users, >> >> I have the decomposition error. I have tried to red

[gmx-users] decomposition error

Dear Grimaces Users, I have the decomposition error. I have tried to reduce the number of cores but still have the same problem. In my conf.gro, the cell size is about 5.5x5.5x5.5 but I do not know what the minimum cell size of 1.875nm. Would you please give me some comments or relevant topics

[gmx-users] topology file format

Dear Grimaces Users, I have a simple question about topology file format. What does "funct" mean in [ bonds ], [ angles ], and [ dihedrals ] terms? Would you please link me where I can find the topology file format meaning? Thank you. -- Gromacs Users mailing list * Please search the

[gmx-users] Two molecules in a single topology file

Dear Gromacs Users, I have a question to create a topology file with tabulated potentials. I have two molecules in coarse-grained beads. The first molecules are 5 beads and 3 types (A-B-C-B-A), and the second molecules are 3 beads and 2 types (D-E-D). A-B bond potential tabulated in

[gmx-users] two molecules in a single topology file

Dear Gromacs Users, I have a question to create a topology file with tabulated potentials. I have two molecules in coarse-grained beads. The first molecules are 5 beads and 3 types (A-B-C-B-A), and the second molecules are 3 beads and 2 types (D-E-D). A-B bond potential tabulated in

[gmx-users] atom name 1 in topol.top and conf.gro does not match

Dear Gromacs Users, I am trying to build topology file containing two different molecules (A molecule, and B molecule) "A" and "B" molecule contain three beads each. "A" molecules start from 1 to 600, and then "B" molecules start from 601 to 900 in conf.gro file. I created topol.top file

[gmx-users] error about x of the xxx bonded interactions could not be calculated ....

Dear Gromacs Users, I am simulating coarse grained polymer systems with tabulated potential (A B C D types). To obtain pair potentials, Iterative Boltzmann Inversion is used with Gromacs. After 14 step (each step runs 1 ns (100) with time step 1 fs - 0.001), the simulation had failed

Re: [gmx-users] error about x of the xxx bonded interactions could not be calculated ....

ons on two-particle systems to verify you can reproduce trivial > energies and forces. > > Mark > > On Fri, 29 Jan 2016 17:17 Chang Woon Jang <changwoonj...@gmail.com> wrote: > > > Dear Gromacs Users, > > > >I am simulating coarse grained polymer system

Re: [gmx-users] Error - syntax

ards, Changwoon Jang On Mon, Jan 25, 2016 at 1:34 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > See > http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx > > Mark > > On Mon, 25 Jan 2016 19:19 Chang Woon Jang <changwoonj...

[gmx-users] Visualization of conf.gro and confout.gro

Dear Gromacs Users, I did NPT simulations with a system containing 15000 atoms of polymers. Initially, conf.gro was visualized in VMD and showed all connections are OK. However, the confout.gro (final output configuration) seems to look bad. Some of bonds are disconnected at the outer surface

Re: [gmx-users] How to adjust the box size to correct density?

nsity 543.21 > kg/l of the solvent and get a new scaled.gro file, I use this command: > > $ gmx editconf -f box.gro -density 543.21 -o scaled.gro > logfile > > > On Tue, Jan 5, 2016 at 7:05 PM, Chang Woon Jang <changwoonj...@gmail.com> > wrote: > > > Dear Gromacs Users, &g

[gmx-users] How to adjust the box size to correct density?

Dear Gromacs Users, I have a low density polymer system initially. I would like to fit the correct liquid density using NPT simulation. I used Pcoupl=berendsen for 22 ns but the box size in confout.gro is still the same as the input size of conf.gro. Initial in conf.gro (10.0 10.0 9.8) output

Re: [gmx-users] How to adjust the box size to correct density?

you. Best regards, Changwoon Jang On Tue, Jan 5, 2016 at 1:44 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/5/16 1:42 PM, Chang Woon Jang wrote: > >> Dear Abhishek Khetan, >> >>Thank you for your answer. It means that Gromacs does not automaticall

[gmx-users] how to adjust the box size to correct density?

Dear Gromacs Users, I have a low density polymer system initially. I would like to fit the correct liquid density using NPT simulation. I used Pcoupl=berendsen for 22 ns but the box size in confout.gro is still the same as the input size of conf.gro. Initial in conf.gro (10.0 10.0 9.8) output

Re: [gmx-users] how to adjust the box size to correct density?

> > Look at what md.log says about the value for pcoupl it read from your .tpr. > :-) > > Mark > > On Tue, Jan 5, 2016 at 9:39 PM Chang Woon Jang <changwoonj...@gmail.com> > wrote: > > > Dear Mark, > > > > I obtained the tpr file with gro and topolog

Re: [gmx-users] How to adjust the box size to correct density?

Dear Justin, Please take a look at the file. I modified mdp file provided from VOTCA tutorial. I think that mdp file is ok. Thank you very much. Best regards, Changwoon Jang On Tue, Jan 5, 2016 at 2:45 PM, Chang Woon Jang <changwoonj...@gmail.com> wrote: > Dear Justin, > &g

Re: [gmx-users] How to adjust the box size to correct density?

= 0 userint3 = 0 userint4 = 0 userreal1= 0 userreal2= 0 userreal3= 0 userreal4= 0 On Tue, Jan 5, 2016 at 2:53 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/5/16 2:51 PM, Chang

Re: [gmx-users] how to adjust the box size to correct density?

at 3:07 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Tue, Jan 5, 2016 at 7:15 PM Chang Woon Jang <changwoonj...@gmail.com> > wrote: > > > Dear Gromacs Users, > > > > > > I have a low density polymer system initially. I would l