[gmx-users] question about dihedral constraints

Dear Gromacs Users, I want to use dihedral constraint in gmx. I directly type the following onto my topol.top file : -- [ dihedral_restraints ] ; ai ajakal type label phi dphi kfac power ; phi C'(n-1) - N - CA - C' 506505 502503

[gmx-users] Re: help with improper angle in gmx

Thanks for your reply, Justin! I knew that gmx use as the follows for opls aa: ; Improper OPLS dihedrals to keep groups planar. ; (OPLS doesnt use impropers for chiral atoms). ; Since these functions are periodic of the form 1-cos(2*x), they are actually ; implemented as

[gmx-users] Re: help with improper angle in gmx (Justin Lemkul)

Table 5.5 does list the option of use harmonic type potential for improper dihedral. (f. tp =5) But I am confused how to build this on the ffbond.itp file and manu is not clear about this. Do you think that in the case of OPLS AA, the periodic improper dihedral is the ONLY option? Thanks a lot

[gmx-users] Re: gmx-users Digest, Vol 104, Issue 24

Dear Tomas, Thanks for your information! I look at the website you mentioned: http://virtualchemistry.org/molecules/110-02-1/index.php The *top file is available and the atom opls-aa types are assigned on *top file. But I can not find these parameters of dihedral angles from the default gmx

[gmx-users] 9-oder cosine series of dihedral angle

proper dih. multi dihedrals 4 9 There is not detailed explanation about the format of these assignment in ffbonded.itp of oplsaa.ff *Can any one give an explanation about the format of typing these parameters for 9-oder cosine series dihedral angle?* Thanks, Tom

Re: [gmx-users] Free energy calculations with BAR and TI

can either edit the code and recompile gromacs or you substitute the temperatures with SED to a temperature nearly the same, 298 for example. Ah, here is the link: http://gromacs.5086.n6.nabble.com/problem-with-g-bar-td4633215.html Best Tom Kirchner On 11/02/2012 10:46 AM, Ignacio Fernández

[gmx-users] Getting the constraint force from the LINCS algorith

the distance on the ions, I would like to use that. Many thanks in advance, Best Tom Kirchner -- 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

[gmx-users] Ligand Internal energy

I am trying to differentiate between several binding poses for a protein ligand complex. Initially I tried the LIE method however its results do not followed the expected trend based on experimental data. I then looked at the raw interaction energies between the ligand and its environment

[gmx-users] Re: Ligand Internal energy

I have been avoiding TI or FEP as I doubt my ligand parametrisation is good enough to warrant the effort. What I am trying to do is get a rough method working as a secondary screen in a lead optimisation effort. I am not trying to be perfect, I am just trying to be better than docking at this

[gmx-users] RE: Re: potential energy

as LIG-rest? All the best, Tom On 14/08/2012 11:07 AM, Tom Dupree wrote: Greetings all, Can I easily obtain the potential energy for a energy group rather than the whole simulation cell? Yes. See manual 3.3 and 7.3.8. But below you imply you're already doing this. You can make custom groups

[gmx-users] RE: RE: Doubts over g_lie usage

. At least RF gives the full electrostatic force out to the cut off. Have fun, Tom The explanation really helps me understand LIE much more clearer. What's the issue if I have used PME coulombtype? I have actually used PME. Thanks, Peterson J -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] RE: RE: RE: Doubts over g_lie usage

interaction energies for each frame in your trajectory that you save co-ordinates for, so it is much, much, faster than redoing the calculations. Have fun, Tom Thanks for that explanation. I would like to know this with little more detail. What do you mean by RF-0 and which cut-off value are you talking

[gmx-users] potential energy

may be one. However any changes in ligand potential energy are going to be dwarfed by protein and water changes. Have fun, Tom -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search

[gmx-users] RE: Doubts over g_lie usage

by Aquvist et al to help with this. Individual average values can be calculated using the LJ and Coul energies/forces from your energy file and following the LIE equation. Beware of using g_lie if you have used PME for your electrostatics. Have fun, Tom Hello everyone, I have a doubt about LIE

[gmx-users] g_lie reproducibility (g_lie is lying)

noticed is that when calculating the average g_lie uses the final value twice, is there a reason for this? e.g. 994 24.9397 996 43.3382 998 40.5714 1000 40.5585 1000 40.5585 All the best, Tom -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] RE: Re: g_lie reproducibility

, and the second last time point has different values. This is a single run so I don't think I should have concatenation issues? I just checked the counts and there are 476 time points in the energy file and 477 in the g_lie file. All the best, Tom On 14/06/2012 3:56 PM, Tom Dupree wrote: Greetings all, I

[gmx-users] bond autocorrelation function

Hello Does gmx provide any script to calculate autocorrelation function for a defined bond (not hydrogen bond autocorrelation function,g_hbond) ? Thanks a lot for the information! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] RE: LIE methodology check

to build the .tpr file? All the best, Tom ___ Message: 2 Date: Mon, 21 May 2012 03:26:07 + From: Tom Dupree t.dup...@unsw.edu.au Subject: [gmx-users] LIE methodology check (mdrun -rerun cutoffs and box vectors) To: gmx-users@gromacs.org gmx

[gmx-users] LIE methodology check (mdrun -rerun cutoffs and box vectors)

on a shape when viewed in VMD? (both are rhombic prisims). All the best, Tom -- 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] polarizable ff and free energy calculation

F_POLARIZATION: if (qS != atom[aS].qB) gmx_fatal(FARGS,polarize can not be used with qA != qB); If anybody knows, how to correct this, I would be very grateful. Moreover I'm wondering about the physical meaning of the if-statement. Best Tom PS: I also attached a minimal system, which

[gmx-users] polarizable ff and free energy calculation

this, I would be very grateful. Moreover I'm wondering about the physical meaning of the if-statement. Best Tom -- 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

[gmx-users] Using polarizable ff for ions in conjunction with free energy calculation

for non-polarizable ff. If someone could help me, I would be very grateful. Best Tom -- 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

Re: [gmx-users] Problem with g_dipoles and SPCE water

On 04/10/2012 12:00 PM, gmx-users-requ...@gromacs.org wrote: On 2012-04-10 11:16, Tom Kirchner wrote: On 04/10/2012 11:10 AM,gmx-users-requ...@gromacs.org wrote: On 2012-04-10 09:57, David van der Spoel wrote: On 2012-04-10 09:43, Tom Kirchner wrote: Hi all, I want

[gmx-users] Problem with g_dipoles and SPCE water

there. Best regards Tom ;== run control === integrator = md tinit = 0 dt = 0.002 ; time step [ps] nsteps = 1000 ; number of steps comm_mode = Linear

Re: [gmx-users] Problem with g_dipoles and SPCE water

On 04/10/2012 11:10 AM, gmx-users-requ...@gromacs.org wrote: On 2012-04-10 09:57, David van der Spoel wrote: On 2012-04-10 09:43, Tom Kirchner wrote: Hi all, I want to test the g_dipoles tool and made a 20 ns simulation with SPC/E water. Sadly the result for the dielectric constant

[gmx-users] Re: RE: problem with g_bar

is of type real * make[3]: *** [gmx_bar.lo] Error 1 Best, Tom On 03/20/2012 03:15 AM, gmx-users-requ...@gromacs.org wrote: -- Message: 3 Date: Mon, 19 Mar 2012 18:34:31 +0100 From: Berk Hess g...@hotmail.com Subject: RE: [gmx-users] problem with g_bar To: Discussion list

[gmx-users] problem with g_bar

in the function header? I appreciate any hints. Best regards Tom -- 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)subscribe

[gmx-users] g_bar bug with temperature

, this number is also written in the .xvg files and the same for all of them. An older setup worked fine a the temperature of 300 K. After I changed the temperature of my new files also to 300 K, g_bar now works. Is it possible, that g_bar can not handle real numbers? Best Tom Kirchner -- gmx-users

[gmx-users] how to use charmm ff in gmx and carbohydrate forcefield

them to *itp and *rtp file? Thanks a lot for the information! Tom -- 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

[gmx-users] Re: charmm27 in gromacs

Got it. Thanks a lot for the help! -- 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)subscribe requests to the list. Use the

[gmx-users] charmm27 in gromacs

Dear Gmx Developer or Users, Can anyone explain which section is for the parameters of improper dihedral angle on the file of ffbonded.itp ? On the file of ffbonded.itp, there is not any comment to differentiate the proper and improper dihedral angle. E.g. on thie file of ffbonded.itp in the

[gmx-users] Re: improper dihedral angle in charmm and opls aa (Mark Abraham)

is sometimes described twice despite of the difference in the atoms' sequence. Suposed for an unkown molecule, how to assign them on rtp file? Can you give some introduction or show somewhere that has the document? Gromacs menu does not document about this. Thanks for advance! Tom Message: 1 Date

[gmx-users] improper dihedral angle in charmm and opls aa

ND2 CG HD21HD22 ND2 CG HD22HD21 in opls aa for ASN CGCBCA C dih_ASN_chi1_C_C_C_CO CACBCG ND2 dih_ASN_chi2_C_C_CO_N Thanks for advance! Tom PS: the detail is as follows

[gmx-users] topolbuild and charges

Hello Gromacs Users: Any one has the experience of topolbuild? I tried to build *top file with the software of topolbuild ./topolbuild -n lipid -dir /home/computer/Tom/topbuild/topolbuild1_3/topolbuild1_3/dat/gromacs -ff oplsaa I chose oplssaa. But from the generated *top file,* these charges

[gmx-users] topolbuild1_3:Illegal characters for size information line in mol2 file.

Dear Bruce and Gromacs Users, i am a new user of topolbuild. I am trying to use topolbuild to build *top file, but there is a fatal error report: --- ./topolbuild -n lipid -dir /home/machine/TOM/Study/topbuild/topolbuild1_3/topolbuild1_3/dat/gromacs -ff oplsaa

[gmx-users] Re: Fwd: about the pulling

Thanks Justin! On 10/17/11, Justin A. Lemkul jalem...@vt.edu wrote: Tom wrote: Justin you have good experience of pulling. If you have time, please help with this publling problem: abrupt change in sign of 1dZ on output file: pullx.xvg. Thanks a lot! I already commented: http

[gmx-users] how to calculate the force between two groups

different groups. Is there any cunning way to do it. Thanks, Tom -- 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)subscribe

[gmx-users] Re: how to calculate the force between two groups (Mark Abraham)

for certain pair of groups! Tom On 31/10/2011 4:05 AM, Tom wrote: Dear Gromacs Users, I have a question about how to ouput the force between two groups. Suppose the system consists of the groups: A, B, C and D. I need the force only between the groups A and B. g_traj looks only to be able

[gmx-users] about the pulling

Thanks a lot for the information! Thanks, Tom -- 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)subscribe

[gmx-users] Fwd: about the pulling

Thanks a lot for the help! Tom -- Forwarded message -- From: Tom dna...@gmail.com Date: Sun, 16 Oct 2011 23:02:09 +0800 Subject: about the pulling To: gmx-users gmx-users@gromacs.org Dear Gromacs Users or Developers, I am using the pulling the COM of object

[gmx-users] angular velocities in gromacs?

Dear Gromacs User, Gromacs *trr file has the velocities. They are for translational motions. But how can we get the angular velocities? Thanks for the information! Tom -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] Single long simulation versus multiple short

to measure and yet ligand position/conformation continues to change throughout the simulation. Tom Widya Desmarani wrote: Dear gromacs user, I have been trying to look for an answer for my following question from our forum but still couldn't manage to find one. Probably it is trivial but I am

[gmx-users] Question about Electrostatic field in Gromacs

]*t); } } - Thanks, Tom, PS: the source code of of sim_util.c for the part of calc_f_el is attached here: * calc_f_el calculates forces due to an electric field. * * force is kJ mol^-1 nm^-1 = e * kJ mol^-1 nm^-1 / e * * Et[] contains

[gmx-users] External Electric field in Gromacs

[m].a[0]*t); } } else { Ext[m] = 1.0; } -- What is meaning of exp part? How to use the functionality of this subroutine by adding the parameters in mdp file? Thanks, Tom PS: The details of the source code was pasted in my

[gmx-users] pull direction of steered MD in Gromacs

Dear Gromacs Users, Can you assign any pulling direction in Gromacs rather than only using the axial x/y/z direction? pull_dim= N N Y Can we assign sth. like a vector in gromacs? Thanks, Tom -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

[gmx-users] Position restraints

matrix over multiple molecules? Or is there a better way of achieving my desired result? (302 atoms across 2 (6) chains constrained in their relative positions) All the best, Tom Fatal error: [ file subset.itp, line 145 ]: Atom index (5222) in constraints out of bounds (1-5149

[gmx-users] Re: Largest charge group radii for Van der Waals; Largest

this to avoid any mistake for the continued simulation? Tom It is also possible that the charge group is split across PBC, causing it to be broken. In this case, nothing is wrong. Using a plain cutoff, however, generally is very wrong... -Justin -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Largest charge group radii for Van der Waals; Largest charge group radii for Coulomb

) is larger than rlist (1.20) --- Is there anyone who can help see why different version mak such problem? How to solve the problem? Thanks a lot! Tom -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] g_covar eigenval.xvg

though. I have searched the archive and can't seem to find any information on this. Does anyone have any experience with this problem? My only thought is to rewrite the .trr and .tpr files with out the solvent and try again, if this is possible? Thanks for any help, Tom

[gmx-users] GROMACS installation query

read this as GCC 4.2.x and greater should be fine. (confirm/deny?) Thank you for your time, Tom -- 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

Re: [gmx-users] combine two gro into one

Or you can do the renumbering through feeding the file through editconf. Tom Justin A. Lemkul wrote: Sikandar Mashayak wrote: yeah I know its simple, but only concern I have is that, the index of atom/residue in two files may not be in agreement, so I have to change/shift index of atoms

[gmx-users] Potential energy of a single amino acid residu

in advance, Tom ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www

Re: [gmx-users] Potential energy of a single amino acid residu

I get the following list: Angle Proper-Dih. Ryckaert-Bell.LJ-14 Coulomb-14LJ-(SR) LJ-(LR) Coulomb-(SR) Coul.-recip. Potential Kinetic-En. Total-Energy Temperature Pressure-(bar)Box-X Box-Y Box-Z

Re: [gmx-users] Carbon Nanotube Simulations

improvements to the x2top program which may be helpful. If not you may need to make one for your molecule. ,Tom On 3/26/07, Mark Abraham [EMAIL PROTECTED] wrote: George Abadir wrote: Hi, I am using Tubegen to generate a PDB file for carbon nanotubes. When I use the x2top command I get

[gmx-users] grompp problem

... so what can be the problem here? Tom ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED

Re: [gmx-users] grompp problem

$ editconf -bt cubic -f sh2_pep.gro -o sh2_pep.gro -c -d 0.9 -bash-3.00$ genbox -cp sh2_pep.gro -cs spc216.gro -o sh2_pep_b4em.gro -p sh2_pep.top -bash-3.00$ grompp -f em.mdp -c sh2_pep_b4em.gro -p sh2_pep.top -o sh2_pep.tpr it then crashes here Tom

re:Re: [gmx-users] grompp problem

of the gromacs website. Is there a online explanation of the format and how new entries can be added? I retrieved all information on PTR from the PRODRG server. Isn't there some way to directly copy and paste this information in the confuguration files? Below the PTR info obtained from PRODRG Tom

re:Re: [gmx-users] how to add a PTR residue into the gromacs simulations

I suspect that in order to have pdb2gmx find the modified files, Tom needs to make a full copy of the gromacs/share/top directory in his own filespace, set the environment variable GMXLIB to that path, and then to edit as necessary. Are there any examples online which I could use as a guide

[gmx-users] how to add a PTR residue into the gromacs simulations

writing privileges for these files on our University cluster. Is there any other (easy) way to resolve this? Tom ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests

Re: [gmx-users] intel compiler + amd64: help needed.

Can you try to generate a backtrace for the mknb crash using gdb, in case this offers some insight?$ gdb mknbgdb r -software_invsqrt...gdb bt(backtrace output appears here)--TomOn May 31, 2006, at 11:33 AM, Jones de Andrade wrote:Hi David. First, thanks for your time. ;) Unfortunatelly, it seems

Re: [gmx-users] Drug Enzyme Tutorial - mdrun segmentation fault

This is probably the result of a bug in 3.3, fixed in 3.3.1. Setting pme_order = 4 is a workaround in case you don't want to upgrade to 3.3.1. --Tom On Apr 19, 2006, at 11:05 AM, Zorzan Simone wrote: Hi all, I am trying to do the Drug Enzyme tutorial (trp_drug_tutor.pdf), on a linux

Re: [gmx-users] Error in compiling gromacs in SGI IRIX6.5

A wild guess: SGI's compiler doesn't support some language feature or other in the same way as expected by the GROMACS source code. So, if you have gcc installed, you might try compiling using that. setenv CC `which gcc` ./configure --put-your-parameters-here --Tom On Apr 3, 2006, at 8:32

Re: [gmx-users] cluster

In your em.mdp file, make sure that the cpp variable is set to the location of your C preprocessor binary. To find out where it is, type which cpp at the command line. --Tom On Apr 2, 2006, at 1:18 PM, Kushal Seth wrote: hi all ! I am trying to run the following command - grompp -np 2

Re: [gmx-users] Error: relative constraint deviation after LINCS

Sorry, but the right way to do it is to recompile GROMACS. Annoying, yes, but necessary :) --Tom On Mar 30, 2006, at 1:55 AM, raja wrote: Dear all, Thanks for your thoughts and suggestions. Please tell me how to update that patch,pme.c in already installed gromacs program. I mean to ask

Re: [gmx-users] pdb2gmx illegal instruction

Certainly you should consult your documentation, but one possibility is: mpirun -np 8 mdrun_mpi -np 8 -s pr -o pr -c after_pr -e pr -g pr -v - N 8 --Tom On Mar 21, 2006, at 6:48 PM, Erik Lindahl wrote: mdrun_mpi -np 8 mdrun -np 8 -s pr -o pr -c after_pr -e pr -g pr - v -N 8