[gmx-users] Is Gromos force field 45a3 out of dated?

Hello, I submitted a paper and get rejected immediately by editor because of the following comment. "The simulations described here rely on an outdated force field (Gromos 45a3) and I suspect that the partial unfolding described here is at least in part due to force field artifacts. " Our simula

[gmx-users] Counting non-bonding interaction

Hi Is there any function counting non-bonding interaction with Gromacs ? Thanks Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't

[gmx-users] Counting number of non-bonded interactions ?

Hi Is there any function to count number of non-bonded interactions with Gromacs ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting

[gmx-users] How to calculate RMSD per residue with Gromacs ?

Hi How to calculate RMSD per residue with Gromacs ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscrib

[gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ?

Message: 1 Date: Thu, 26 May 2011 19:54:29 -0700 From: Chih-Ying Lin Subject: [gmx-users] Domain Motion => How do get the rotational axis fromeigenvectors ? To: gmx-users@gromacs.org Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi I want to protein'

[gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ?

Hi I want to protein's domain motion. I use g_covarandg_anaeig to get the eigenvectors. How can i get the rotational axis of which protein do its domain motion from those eigenvectors? I found the papers and the authors plot its rotational axis of domain motion. How did they make it ?

[gmx-users] Re-compile Gromacs Program?

Hi I found the Gromacs Program could not do the parallel computing since the staff of the compter center in my school upgraded the intel compiler to v 12, and rebuilt the mpich build with intel. I requested them to recompile the Gromacs Program but they rejected and they answered that the updated i

[gmx-users] Diffusion Coefficient

Hi I calculated the diffusion coefficient for lysozyme and get ~4x1e-6 (cm2/s) But, the experimental data is around 1x1e-6 (cm2/s). How could I explain for this discrepency? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] ZN2+ qtot 1.233e-06 ?

Hi I issued "pdb2gmx with G45a3 force field" on the "bovine carbonic anhydrase" From the .top value, the ZN+2 is given qtot 1.233e-06 .. 2611 ZN2+257 ZN ZN 1137 2 65.37 ; qtot 1.233e-06 I am confused with the charges. Isn't ZN+2 carrying +2 cha

[gmx-users] ZN2+ qtot 1.233e-06 ?

Hi I issued "pdb2gmx with G45a3 force field" on the "bovine carbonic anhydrase" >From the .top value, the ZN+2 is given qtot 1.233e-06 .. 2611 ZN2+257 ZN ZN 1137 2 65.37 ; qtot 1.233e-06 I am confused with the charges. Isn't ZN+2 carrying +2 charges ??

[gmx-users] Standard Procedures to perform MD under High Temperature 498 K, either NVT or NTP ?

Hi I read some papers and many simulations were performed under high temperature to induce the unfolded protein. However, the authors did not mention how they conducted the simulations under high temperature, 498 K. They did not mention which NVT or NPT were adopted for such high temperature. None

[gmx-users] High Temperature 498 K, NVT or NTP ?

Hi At high temperature 498 K, the protein is cooked. For NVT, the volume of the system is much expanded. For NPT, the water evaporated. How do people simulate the condition under high temperature, 498K? THank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/ma

[gmx-users] g_rmsf => average over # of time frames ???

Hi >From source code => gmx_rmsf.c "g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard ", "deviation) of atomic positions ", if (devfn) { /* Calculate RMS Deviation */ for(i=0;(i-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.or

[gmx-users] g_rmsf -res yes ? => should I type "yes" to activate the "average-function" ?

Hi g_rmsf -res yes ? g_rmsf -res no ? should I type "yes" to activate the "average-function"? As i tested "g_rmsf -res", the average is not over time and not over the atoms in the residue. Anyway, how to activate the "average function" ? Thank you

[gmx-users] g_rmsf -res => what does this function work?

Hi >From Manual http://manual.gromacs.org/current/online/g_rmsf.html g_rmsf => optiontypedefaultdescription -[no]res bool noCalculate averages for each residue what does this function work? Thank you Lin -- gmx-users mailing listgmx-use

[gmx-users] g_rmsf -res => does Gromacs do average over time for each residue ?

Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg From manual => it says " Calculate averages for each residue " => does Gromacs do average over time for each residue ? => however, the results did not show difference with and without " -res "

[gmx-users] g_rmsf -res => average over time for each residue?

Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg *-[no]res* bool no Calculate averages for each residue abcrmsf.xvg => average over time for each residue? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please sea

[gmx-users] g_dipole ? =>salt-molecule => Does Gromacs consider counter ions?

-) If I select #12, Gromacs will not consider counter ions to calculate the dipole moment ??? Sorry for disturbing people in the Gromacs mailing list. Thank you Lin On 2010-10-22 00.49, Chih-Ying Lin wrote: > Hi > When I issued the command g_dipole, > the dialog poped out and asked me

[gmx-users] g_dipole ? =>salt-molecule => Does Gromacs consider counter ions?

Hi When I issued the command g_dipole, the dialog poped out and asked me to select a group. 1. system 2. protein . 11. solvent 12. the rest of the salt-molecule except its counter ion 13. counter ions (CL-) If I select #12, Gromacs will not consider counter ions to calculate the di

[gmx-users] g_dipole ? =>salt-molecule => the relative position of counter ions to the rest of salt-molecule matters ???

HI As Timo M.D. Graen described "As long as the system is neutral, the reference point will not affect the calculation result of the dipole moment for the system." On the other hand, I also play around the small salt-molecule as Timo M.D. Graen suggested. "take two ions for a start, Na+ and Cl-,

[gmx-users] g_dipole ? => dipole moment => trans-structure is more hydrophobic than the cis-structure ?

Hi In one paper, the salt-molecule has two structures, trans and cis. The sentence in the paper is that trans-structure is more hydrophobic than the cis-structure without providing the value of the dipole moment. I wonder know if the value of dipole moment is the main indicator to decide if tran

[gmx-users] g_dipole ? => The salt molecule => The discrepancy of dipole moment between my calculation and GROMACS

I wouldn't include the bromide if I were you, as it just adds noise, because it can move around freely. You seem to be interested in the change in dipole moment in the cation only, anyway. Cheers, Tsjerk On Oct 21, 2010 7:02 AM, "Chih-Ying Lin" wrote: HI dipole moment = 48.0 sum of

[gmx-users] g_dipole ? => The salt molecule => The discrepancy of dipole moment between my calculation and GROMACS

HI dipole moment = 48.0 sum of q_i x_i x_i is the atomic position. I did not include the counter ion of the salt molecule in my calculation. The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans. Here "A" are a string of atoms, most of them are carbons. For the cis-structur

[gmx-users] g_dipole ? => salt molecule in water => should I include counter ions in my calculation?

HI 48.0 sum of q_i x_i x_i is the atomic position. For the salt molecule in water, should I include counter ions in my calculation ? Or, only the rest of the salt molecule except the counter ions? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/

[gmx-users] g_dipole ? => salt molecule in water => what is the the displacement vector pointing from the negative charge to the positive charge?

to one counter ion and the rest of the molecule in water? http://en.wikipedia.org/wiki/Bond_dipole_moment http://en.wikipedia.org/wiki/Electric_dipole_moment Thank you Lin On 2010-10-20 06.06, Chih-Ying Lin wrote: > > > > > Hi > molecule dipole is 48.0 sum of q_i x_i &

[gmx-users] g_dipole ? => what is the bond length of the ionic bond in the dipole moment calculation?

st year physics book it will contain very similar information. On 10/19/2010 05:39 AM, Chih-Ying Lin wrote: > > > Hi > According to the following website, > > http://en.wikipedia.org/wiki/Bond_dipole_moment > > > \mu = \delta \, d. > The bond dipole is modeled as

[gmx-users] g_dipole ? => ionic bond => how to determine the direction of ionic bond dipole moment ?

calculator in about 10min. Do not worry about the reference point as long as your system is neutral, just set it to (0,0,0). Otherwise, take any kind of first year physics book it will contain very similar information. On 10/19/2010 05:39 AM, Chih-Ying Lin wrote: > > > Hi > Acco

[gmx-users] g_dipole ? => Calculate bond dipole moment for a molecule of multiple atoms by hand?

ou Lin On 2010-10-18 03.30, Chih-Ying Lin wrote: > HI > I confined one molecule in the center of box and issue the g_dipole command. > The average dipole moment is still around 32. > It is the molecule with 33 atoms / united atoms of most carbon groups, > isn't the dipole

[gmx-users] g_dipole ? => dipole moment ?

s center of atom from the mass center of the molecule? 4. What does the large charge separation mean? Do you mean the charged molecule? Or, Do you mean the molecule with a long carbon chain? Thank you Lin On 2010-10-18 03.30, Chih-Ying Lin wrote: > HI > I confined one molecule in the c

[gmx-users] g_dipole ? => dipole moment ?

oment around 32 is acceptable? Thank you Lin On 2010-10-16 21.36, Chih-Ying Lin wrote: > > Hi > I issue the g_dipole command on Gromacs => And, the following > information is shown. > There are 10 molecules in the selection, > Does the Average =32.1611 refer to the ave

[gmx-users] g_dipole ? => dipole moment ?

Hi I issue the g_dipole command on Gromacs => And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time?

[gmx-users] Force Field => Residues PHE, TRP, TYR, HIS ?

HI Residues PHE, TRP, TYR, and HIS are carrying "Rings", or say pi bonds. How does the Gromacs deal with polarity for all this four residues? Is a single charge assigned for each atom on the center of atoms of the four residues ? Is pi bond given for the four residues in the force field? Tha

[gmx-users] g_sas => calculate the SASA for each residues ?

Hi How can I calculate the SASA for each residue ? >From Manual => "The program will ask for a group for the surface calculation and a group for the output." When I issue the command => g_sas -f abc.gro -s abc.tpr -n Residue1.ndx -o SASA.xvg => Gromacs will pick Residue1.ndx as both a grou

[gmx-users] dipole moment of molecule of trans and cis azobenzene ?

HI >From David => dipole moment = mu = sum_i q r. is that sum of partial charges * r ? what is the " r " ? Thank you Lin On 2010-08-26 18.59, Chih-Ying Lin wrote: > > Hi > The partial charges of the trans and cis azobenzene are given as point > charges lied

[gmx-users] g_sas => protein interface => HALF of ( A+B-AB) ?

Hi Execute g_sas to get protein interface >From David => "If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB" WHy not HALF of (A+B-AB) ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/li

[gmx-users] dipole moment of molecule of trans and cis azobenzene ?

HI The charges of azobenzene from the authors, who made the QM/MM simulations and fit some experimental data about the azobenzene. Thank you Lin On 2010-08-26 18.59, Chih-Ying Lin wrote: > > Hi > The partial charges of the trans and cis azobenzene are given as point > charges

[gmx-users] dipole moment of molecule of trans and cis azobenzene ?

Hi The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center in my MD simulation. It is supposed that the real molecule of trans-azobenzene has a lower dipole moment than the cis one. So, the real molecule of trans-azobenzene is supposed to be more hy

[gmx-users] g_sas => protein interface => HALF of ( A+B-AB) ?

Hi Execute g_sas to get protein interface >From David => "If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB" WHy not HALF of (A+B-AB) ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/li

[gmx-users] g_gyrate -p => the radii of gyration about the principal axes ?

tein molecule is a standard process ? => I mean the principal axes of the protein molecule is fixed, right ? => I mean the math of the principal axes of the protein molecule is defined all over the world , right ? Thank you Lin On 2010-08-14 23.49, Chih-Ying Lin wrote: >

[gmx-users] g_gyrate -p => the radii of gyration about the principal axes ?

Hi To Calculate the radii of gyration about the principal axes I use the command g_gyrate -p For lysozyme , I got => 0.922754 1.22249 1.25603 but in some paper, the authors got => 0.660 0.833 0.991 It is a quite difference. what is the definition of the radii of gyration about the

[gmx-users] g_gyrate -p => Calculate the radii of gyration about the principal axes

Hi To Calculate the radii of gyration about the principal axes I use the command g_gyrate -p For lysozyme , I got => 0.922754 1.22249 1.25603 but in some paper, the authors got => 0.660 0.833 0.991 It is a quite difference. what is the definition of the radii of gyration about the

[gmx-users] trjconv => -[no]vel => print out the velocity ?

Hi Trjconv => with option "- [no] vel " what does the bracket "no" mean ? with the following command, trjconv -f MD.trr -s MD.tpr -vel -o MD-test.gro the velocity is not print out on MD-test.gro. How to print out both the velocity and trajectory at the same time from .trr file? THank y

[gmx-users] g_sas -pbc ???

Hi g_sas By default, periodic boundary conditions are taken into account. How does g_sas deal with periodic boundary conditions effects? ? ? Take trjconv an example, I have tried trjconv -pbc ( nojump , whole, atom... ) or, trjconv -center . I could not get what i wanted. Thank you Lin -- gmx

[gmx-users] g_sas => protein and ligand aggregate interface area ?

HI As David said, => How to compute protein-protein interface area? "If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB" I want to calculate protein and ligand aggregate (small micelle of ligand) interface area. Is it the same step as calcu

[gmx-users] g_sas => micelle ?

HI how to calculate SASA of micelle using g_sas? i put -n -micelle-index.ndx , where micelle-index.ndx includes all of the atom numbers of micelle. if micelle is not compact enough but there are no water molecules inside the micelle, will g_sas calculate the vacancy part inside the micelle? Or,

[gmx-users] DSSP=> how to edit .eps file

HI How to pass an .m2p file to xpm2ps to change the dimensions of the plot, data point size, etc. ??? Thank you Lin Chih-Ying Lin wrote: > > Hi > With the following two commands, > > do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xv

[gmx-users] g_sas

Hi >From David, "If you select a group consisting of a single residue in a protein the SAS will be computed as if the rest of the protein is not there. Very useful when you want to compute protein-protein interface areas." => therefore, if i select a group consisting of a single residue, which is

[gmx-users] g_sas

Hi g_sas computes hydrophobic, hydrophilic and total solvent accessible surface area. I chose => protein for calculation group => protein for output group what does it define "hydrophobic solvent accessible surface area"? => does that, the surface area, enclose the hydrophobic atoms/

[gmx-users] DSSP=> how to edit .eps file

Hi With the following two commands, do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xvg xpm2ps -f secondary-structure.xpm -o secondary-structure.eps With GIMP, i can see the secondary structure plot. The legend indicates the color of different second str

[gmx-users] g_sas

HI THe command => g_sas_mpi -f 6LYZ-MD566500.xtc -s 6LYZ-MD566500.tpr -o solvent-accessible-surface.xvg -oa atomic-sas.xvg -or residue-sas.xvg In the solvent-accessible-surface.xvg => @ s0 legend "Hydrophobic" @ s1 legend "Hydrophilic" @ s2 legend "Total" @ s3 legend "D Gsolv" What does "Hydrop

[gmx-users] DSSP=> how to edit .eps file

HI 1. dssp -n index.ndx => only atom numbers of one residue in the index.ndx => can dssp decide the exact second structure for the only one residue without considering other residues of protein? => can i get the same second structure for the residue with [ dssp -n one-residue.ndx ] and [dssp -n p

[gmx-users] DSSP => how to edit .eps file

HI After running DSSP, .eps files are created. We can see the second structures of the all residues. I only want to see the change of the second structures of some specific residues. How can i do it? Also, how can I change the thickness of the color band for each residue? The logo indicates the co

[gmx-users] g_sas

Hi The command g_sas => Select a group for calculation of surface and a group for output What is the difference between "a group for calculation of surface" and "a group for output"? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] trjcat and trjconv

Hi file1.xtc and file2.xtc are two consecutive MD trajectory files of the same simulation system. file1.xtc = 238 frames (t= 0.0 to t= 476.0) file2.xtc = 366 frames (t= 0.0 to t= 732.0) trjcat -f file1.xtc file2.xtc -cat -o file3.xtc file3.xtc = 604 frames =23

[gmx-users] Backbone and MainChain

Hi >From Gromacs Manual: - Backbone: all protein backbone atoms (C-alpha, N, C) - MainChain: backbone atoms, plus the carbonyl oxygens The following is part of .gro file. I listed the atom number, are those all correct ? C-alpha: 161,170,179 N:158,163, 172 C: ??? what does this "C" rep

[gmx-users] PH 5.0 ?

HI How to assign charge for the residue of protein at PH 5.0 ? I have Ka values of each residue of protein then i can calculate the overall charge for each residue at PH 5.0 solution. However, how to calculate the partial charges of atoms within the residue of protein at PH 5.0? Thank you Lin --

[gmx-users] grompp - commands

Hi Here are four commands. PART I grompp_mpi -np 16 -v -f md.mdp -c 6LYZ-MD.gro -p 6LYZ.top -o 6LYZ-MD55.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-MD55 PART II grompp_mpi -np 16 -v -f md.mdp -c 6LYZ-MD55.gro -p 6LYZ.top -o 6LYZ-MD155.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-MD155 Will t

[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

Today's Topics: 1. 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken (Chih-Ying Lin) 2. 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken (output file) (Chih-Ying Lin) -- Message: 1 Date:

[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broke

with the addition of ions to your .top file. In your protocol, it's not mentioned. Have you made sure that issue is cleared? Cheers, Tsjerk On Sun, Jan 10, 2010 at 5:25 AM, Justin A. Lemkul wrote: > > > On 1/9/10 10:42 PM, Chih-Ying Lin wrote: >> >> Hi >> I

[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

Hi I did the EM and the potential energy went to the very negative number. But the simulaiton broke in the PR step. Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search befor

[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken (output file)

Hi 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the simulation on Gromacs. System = 6LYZ.pdb + CL- + water molecules Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all. Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step Positio

[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

Hi 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the simulation on Gromacs. System = 6LYZ.pdb + CL- + water molecules Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all. Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step Positio

[gmx-users] simulation broke at 4.0.5 version

Hi I am using Gromacs version 4.0.5. I put one protein in a simulation box with water molecules and CL- only. My simulation broke at the step, Relaxation of solvent and hydrogen atom position. Here are the .top file, command, output of the grommp, pr.mdp. anything wrong here? Thank you Lin *[

[gmx-users] low concentration simulation ?

the same way as if you add ten at a time? Will they aggregate? Will they inherently bind the protein in the same way, or will it be different? " => I don't know, but I assume that will make little difference. Thank you Lin Chih-Ying Lin wrote: > > HI > I am simulati

[gmx-users] low concentration simulation ?

HI I am simulating the protein + ligand + water molecules system. In the experimental work, the concentration of ligand is pretty low, say under 20 mM (avearge 18 ligands attached on one protein) It will be a huge system to create a system with 20 mM and it will take lot of simulation time. Inste

[gmx-users] Simulation Box break into 16 domains => .tpr file is wrong (Gromacs 3.3.3)

Hi, Thanks a lot, Tsjerk ! My simulation is running. I never knew that a discrepancy between the the .top file and .gro, grompp uses the topology information in stead of the coordinate file information. What does issue a set of warnings by grompp ? How do you know the discrepancy between the th

[gmx-users] Simulation Box break into 16 domains => .tpr file is wrong (Gromacs 3.3.3)

-grompp.gro* *6LYZ-solvated.gro => all molecules are intact * and protein is centered. *6LYZ-EM-solvated-after-grompp.gro => protein and water molecules are broken.* ** ** This is the main problem that my simulation box into 16 domains. Thank you Lin ** ** ** Chih-Ying Lin wrote: > >

[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

is no description in the manual that people cannot use -d and -box simultaneously. I visualized the .gro file created by the editconf, the protein is centered in the box as I can see. Thank you Lin Chih-Ying Lin wrote: > > > > Hi > As I posted the command list earlier, to create t

[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

A. Lemkul" Subject: Re: [gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3 To: Discussion list for GROMACS users Message-ID: <4b3e8b11.7040...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Mark Abraham wrote: > Chih-Ying Lin wrote: >> &g

[gmx-users] Gromacs 3.3.3 => what MPI based on ?

Hi There is no domain decomposition with Gromacs 3.3.3. What MPI based on with Gromacs 3.3.3? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don'

[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

Hi Sorry that i have posted the same message for several times. I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total After doing the energy minimization, => the potential e

[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

Hi I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total After doing the energy minimization, => the potential energy is extremely high ( say, ten to the 9th order ) I visua

[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

> > Hi > I used Gromacs version 3.3.3. > My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 > ) > MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total > After doing the energy minimization, => the potential energy is extremely > high ( say, ten to the 9th

[gmx-users] Simulation Break => Due to bad domain decomposition ? (MPI) => Gromacs Version 3.3.3

Hi I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total After doing the energy minimization, => the potential energy is extremely high ( say, ten to the 9th order ) I visual

[gmx-users] Break ? => Position restrained MD

Hi In the position restrain MD, only solvent molecules and hydrogen atoms are allowed to move. I checked the .out file. The max is happened on the atoms inside protein. Why? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Pleas

[gmx-users] clashing happened inside the protein molecule?

Hi Here is my .out file. atoms 366 and 368 are two atoms inside the protein. What is other possible way to solve it ? Thank you Lin relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: atom 1

[gmx-users] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?

Hi what does the max max 597108032.00 (between atoms 366 and 368) mean? is it the max force or max length of the system? where is the max force listed? max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: what does previous, current mean

[gmx-users] some molecule clashing with another ?

--- Potential8.98118e+08 4.53312e+08 0 -3.03617e+07 -1.97304e+09 Kinetic En. 0 0 0 0 0 Total Energy 8.98118e+08 4.53312e+08 0 -3.03617e+07 -1.97304e+09 gcq#119: "Bring Out the Gimp" (Pulp Fiction) Chi

[gmx-users] How to modify or avoid some molecule clashing with another ?

From: "Justin A. Lemkul" Subject: Re: [gmx-users] some molecule clashing with another ? To: Discussion list for GROMACS users Message-ID: <4b3be9b3.8020...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Chih-Ying Lin wrote: > > > Hi > My simulation b

[gmx-users] some molecule clashing with another ?

previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Back Off! I just backed up step0.pdb to ./#step0.pdb.6# Wrote pdb files with previous and current coordinates Terminated Chih-Ying Lin wrote: > > > Hi

[gmx-users] some molecule clashing with another ?

Hi My simulation broke down and the simulation procedues are as follows. 1. center a protein molecule in the simulation box 2. put 20 ligands around the protein with " genbox " command 3. make sure that any atom of the ligands does not overlap on any atom of the protein with Visulization-software

[gmx-users] How to put more solutes into the system ?

system pbc = xyz (minim.mdp) => the system is crystallized with visualization 7. Relaxation of solvent and hydrogen atom positions Run => Position restrained MD => simulation break What is wrong here? How to put another 10 ligands into the simulation box correctly? Thank you

[gmx-users] How to put more solutes into the system ?

ystem pbc = xyz (minim.mdp) => the system is crystallized with visualization 7. Relaxation of solvent and hydrogen atom positions Run => Position restrained MD => simulation break What is wrong here? How to put another 10 ligands into the simulation box correctly? Thank

[gmx-users] How to put more solutes into the system ?

Hi I have a system - solutes with water. The system has been under MD simulation for 100 ns. Now, I want to put more solutes in it. Would you please tell me which command can make it ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] g_msd => The MSD and periodic boundary condition

Hi With the periodic boundary condition, all the recorded coordinates of the atom are within the simulation box. To calculate the MSD, the movement of the center mass of the molecules between this time step with the next time step is calculated without considering the periodic boundary condition. B

[gmx-users] Decreasing MSD of ligand ?

Hi The MSD decrease occurs in the long times. The ligand has bounded to a protein. How can the decrease happen? Thank you Lin Chih-Ying Lin wrote: > > > > HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I > simulate the protein and ligand system and the

[gmx-users] Decreasing MSD of ligand ?

HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I simulate the protein and ligand system and then calculate the MSD of the ligand. Then, i drew the plot of the time evolution of the MSD. But the the MSD decreases as time for some period. I see nothing about my codings. Would yo

[gmx-users] Increase temperature to 550K => simulation techniques ?

e you some insights into what might be wrong. Plenty of groups have successfully been doing high-temperature MD for a number of years. -Justin Chih-Ying Lin wrote: > > Hi > the water model is TIP3P. > > Thanks > Lin > > > > I think the problem is hidden in your wa

[gmx-users] Increase temperature to 550K

other methodological concerns (pressure coupling especially); a thorough search of the literature will give you some insights into what might be wrong. Plenty of groups have successfully been doing high-temperature MD for a number of years. -Justin Chih-Ying Lin wrote: > > Hi > the wa

[gmx-users] Increase temperature to 550K

Hi the water model is TIP3P. Thanks Lin I think the problem is hidden in your water force field model. > The simulation system is merely water + one lysozyme. > I increase temperate to 550K. > > Then, the simulation broke. > The following message is shown. > > MX:hpc0011:Remote endpoint is cl

[gmx-users] Increase temperature to 550K

lincs-iter = 1 lincs-warnangle = 30 Chih-Ying Lin wrote: > HI > The simulation system is merely water + one lysozyme. > I increase temperate to 550K. > > Then, the simulation broke. > The following message is shown. > > MX:hpc0011:Remote endpoint is

[gmx-users] Increase temperature to 550K

HI The simulation system is merely water + one lysozyme. I increase temperate to 550K. Then, the simulation broke. The following message is shown. MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) mpiexec: Warning: task 0 exited with status 1. mpiexec: Warning: tasks 1-2 di

[gmx-users] Long Simulation Time

HI i was reading somewhere.. "simulation will break / terminate when the simulation is running so so long "... Did anyone read the same information? Please refer me the related information since I have no idea where I read this information. How long is long ? How to avoid this? Thank

[gmx-users] Is the time scale of the protein domain motion within nano-second?

Hi Is the time scale of the protein domain motion within nano-second? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before

[gmx-users] trjconv => not get the enough data ?

Hi in my .mdp file, i set up the total 4000 times saving the coordinates of each atom. then, I use the command trjconv -f xx.gro -s xx.tpr -o xx-traj.gro then, i checked the xx-traj.gro file and found there were less than 4000 times of recording coordinates for each atom. say 3600 times of

[gmx-users] g_msd ?

Hi # g_msd_mpi is part of G R O M A C S: # # Giant Rising Ordinary Mutants for A Clerical Setup # @title "Diffusion Coefficients / Molecule" @xaxis label "Molecule" @yaxis label "D" @TYPE xy 00.907803 1 3.5355 2 4.34231 3 3.83589

[gmx-users] Can Gromacs produce the data from NMR?

HI Can Gromacs produce the data from NMR? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post

[gmx-users] template.c

d => ./template < template.in Am I right? Thank you Lin Chih-Ying Lin wrote: > Hi > Following are > 1. template.c > 2. README > 3. Makefile.x86_64-unknown-linux-gnu > > > In the template.c => it includes several GROMACS headers. > #include "statutil.h&qu

[gmx-users] template.c => put the GROMACS headers in the same file ?

Hi Following are 1. template.c 2. README 3. Makefile.x86_64-unknown-linux-gnu In the template.c => it includes several GROMACS headers. #include "statutil.h" #include "typedefs.h" #include "smalloc.h" #include "vec.h" #include "copyrite.h" #include "statutil.h" #include "tpxio.h" If I put t

[gmx-users] template.c

Hi : I have difficulties to understand the following three files, which are in Gromacs Package. 1. template.c 2. README 3. Makefile.x86_64-unknown-linux-gnu Please tell me if I have to do part 3 to compile template.c. Thank you Lin = [ TEMPLATE.C ] ==

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