[gmx-users] Hamiltonian REMD code uploaded in gromacs / user contributions / other software

Assist Prof. Yuguang Mu School of Biological Sciences Nanyang Technological University 60 Nanyang Drive, Singapore 637551 Office: 04s-46 Tel: +65-63162885 Fax: +65-67913856 Email:y...@ntu.edu.sg CONFIDENTIALITY: This email is intended solely for the person(s) nam

RE: [gmx-users] Still model

Dear Chi-Xheng, We have tried GB module in gromacs, but unfortunately we found something wrong with it. What we found is that the results got from gromacs were quite different from those obtained from AMBER codes. We did not check in details why. Yuguang From: gmx-users-boun...@gromacs.org [ma

[gmx-users] cvs version

Hi all, When I use cvs version, pdb2gmx, it shows such error Program pdb2gmx_cvs, VERSION 4.0.99-dev-20100328-954f577 Source code file: pdb2top.c, line: 137 Fatal error: No force fields found (files with name 'forcefield.itp' in subdirectories ending on '.ff') For more information and tips for t

RE: [gmx-users] compiling problem

: [gmx-users] compiling problem Is LAM-MPI's binary in PATH? if you run mpicc from console, will it also show "No such file or directory"? Check LAM-MPI installation. Regards, Yang Ye On Wed, Sep 16, 2009 at 12:39 PM, Mu Yuguang (Dr) mailto:y...@ntu.edu.sg>> wrote: Hi

[gmx-users] compiling problem

Hi, I use git clone git://git.gromacs.org/gromacs.git to get the lastest version and ./bootstrap To generate the configure file Then use ./configure successfully Howeve, after make The error appears as foloowing: mpicc -DHAVE_CONFIG_H -I. -I. -I../../../../src -I/usr/X11R6/include -I/usr/in

[gmx-users] long range restrain

Dear Colleagues, I am using gromacs 4.0.5, when I applied some long-ranged restrains (using NMR restrain tools), it stopped with output: Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd) Howeve

RE: [gmx-users] the temperature effect in the simulation

Do you have water ? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Nicolas Sapay Sent: 2008年11月12日 4:15 To: Discussion list for GROMACS users Subject: Re: [gmx-users] the temperature effect in the simulation He, Yang wrote: > Hi all users, > > When I cha

RE: [gmx-users] settle issue

/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Tuesday, July 29, 2008 2:27 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] settle issue Mu Yuguang (Dr) wrote: > Dear All, > When I try to simulate T

[gmx-users] settle issue

Dear All, When I try to simulate TIP4Pew water box at 298K, and found the density got from gromacs is relative low (983 g/cm3) than the amber (sander) version 994 g/cm3. I cannot find the reason. The parameters for the tip4pew model are identical. When I check some intra-molecular distances, and se

[gmx-users] hybrid or Hamiltonian REMD in gromacs

Dear David, Recently we have developed hybrid or Hamiltonian REMD method by modifying gromacs source code. If interested see our two JCP papers. If you, developers of GROMACS, are interested in including such method in new version of gromacs release. I am very pleased to share the idea here: In R

RE: [gmx-users] Talk slides from the Gromacs Stanford 2008 workshop

Sorry Eric, I cannot see anything. Regards Yuguang ___ 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)subsc

RE: [gmx-users] regarding .gro file

In the last line. Dr. Yuguang Mu School of Biological Sciences 60 Nanyang Drive Nanyang Technological Uiversity Singapre Tel: +65-63162885 email:ygmuATntu.edu.sg -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ananya Debnath Sent: Friday, November 23, 20

RE: [gmx-users] REMD As A Function of Distance Between 2 Chains

Dear Huey Ling, In principle it is applicable. Then such REMD can be termed as Hamiltonian REMD instead of canonical temperature REMD. Dr. Yuguang Mu School of Biological Sciences 60 Nanyang Drive Nanyang Technological Uiversity Singapre Tel: +65-63162885 email:ygmuATntu.edu.sg ___

RE: [gmx-users] charge density of lipid

arge density of lipid Mu Yuguang (Dr) wrote: > No, net charge density estimated from experimental data. what does it mean, how is it measured? you can have nuclear charge minus electron density, but this is not very accurate. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell

RE: [gmx-users] charge density of lipid

] charge density of lipid Mu Yuguang (Dr) wrote: > Dear all, > > How to estimate the charge density of a lipid , the reason we want to do > is that we try a model system to mimic the lipid environment. > > It seems out of GROMACS discussion range, but I believe many Gromacs

[gmx-users] charge density of lipid

Dear all, How to estimate the charge density of a lipid , the reason we want to do is that we try a model system to mimic the lipid environment. It seems out of GROMACS discussion range, but I believe many Gromacs users do lipid simulations. Best regards Yuguang

[gmx-users] Fatal error: more tahn

Dear all, When I use distance constrains(NMR), there happens such errors: Fatal error: More than 8 graph edges per atom (atom 1) I have more than 8 constrains on atom 1. What's reason? Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological U

RE: [gmx-users] Replica Exchange MD ... Exchange rates

That's great. Usually is 30%, of course also depends on how often you let exchange. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.

RE: [gmx-users] PBC problem

option I added is -fix. Note that editconf will still issue a warning about the skewness of the box, but on a 'fixed' structure, that should not occur anymore. Hope it helps, Tsjerk On 5/16/07, Mu Yuguang (Dr) <[EMAIL PROTECTED]> wrote: > Thanks Tsjerk, > Probably because we

RE: [gmx-users] PBC problem

Thanks Tsjerk, Probably because we use pressure coupling and the box size is deformed. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.n

[gmx-users] PBC problem

Hi all, We found some problems in using g_dist or g_minidist to calculate distance in some PBC condition, dodecahedron The output is as followed: Back Off! I just backed up mindist.xvg to ./#mindist.xvg.2# Warning: Triclinic box is too skewed. Box (3x3): Box[0]={ 6.46530

RE: [gmx-users] Can you help me ?

It seems the ions type not set. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php _

RE: [gmx-users] modify C6 directly in FF using sigma and epsilon

Yes. I did this way. I wrote it in small awk script. If you like I can share with it. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.nt

RE: [gmx-users] modify C6 directly in FF using sigma and epsilon

Dear David, In fact I really did as you said. First prepare a top file which explicitly include all bonded and nonbonded terms according to combination rule. In this way that top file can be called stand-alone top file (all the necessary parameters all included). Then you can do what you want. In m

RE: [gmx-users] Error when adding a unnatural amio acid

Please check the xlateat.dat file in share/top/ There is one line in it protein HT1H1 which will automatically change your atom name "HT1" to H1. Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singap

RE: [gmx-users] a small bug?

x.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Thursday, December 21, 2006 11:57 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] a small bug? Mu Yuguang (Dr) wrote: > Hi all > We find that in mdp file, if it is

[gmx-users] a small bug?

Hi all We find that in mdp file, if it is written in this way: ewald_rtol = 1e-5 in fact it is the default value. But grompp cannot recognize it, finally in log file output it will appear: ewald_rtol = 0 And the simulation box will explode. But if it is written in this way: ewald_rt

RE: [gmx-users] Hi...

OPLS-aa force field is good for beta structure, it is not so good for alpha helix study. Amber99f force field is good for alpha helix , but not good for beta structure   Best regards Yuguang   Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological

RE: [gmx-users] CHARMM force field implementation in Gromacs : conversion of periodic into Ryckaert-Bellemans parameters.

That's why I use a second step to modify the created top file to add such specific dihedral angle explicitly in the top file. >I have noticed that both in the Yuguang Mu's and the Mark Abraham's work, >the periodic parameters of dihedral angles have been converted into >Ryckaert-Bellemans ones. I

RE: [gmx-users] the gmxdump reveals less parameters than i expect

Is it because there are two identical parameters? Best regards Yuguang Dr. Yuguang Mu Assistant Professor School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Tel: +65-63162885 Fax: +65-67913856 http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php

RE: [gmx-users] free energy: annihilation

Hi David, Recently I repeated some free energy solvation calculations according to the tutorial by David Mobly. I agree with him that when you do DMSO which has some high partial charges, You should do calculations with Coulomb and VdW separately. Otherwise unphysical results appear. Best regards

RE: Θέμα: Re: [gmx-users] cyclic peptides

If I am not wrong, what you want to do is to build a topological file correctly for a cyclic peptide. You can do this: For example, your peptide has 5 (n=5) aa: CAAAD, You can build easily a linear topology file for a six (n+1) aa peptide chain ( with -ter switch answered by none): CAAADC, the l

RE: [gmx-users] output energies by group

/index.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, August 05, 2006 3:40 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] output energies by group Mu Yuguang (Dr) wrote: > Dear all, > >>&

RE: [gmx-users] output energies by group

Dear all, >> How to output energies of different groups during the MD simulation? >with g_energy, if you have used energy groups in the simulation... No, I mean output the group energies in the flying ( using cut-off, during the simulation, not after the simulation), I think I have to modify the s

[gmx-users] output energies by group

Dear all, How to output energies of different groups during the MD simulation? Best regards Yuguang ___ 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

[gmx-users] diheadral PCA method

Dear All, Some of you want comments on the dihedral PCA analysis. Here I give the link to one comment on that which will appear in Proteins although we do not agree with their main result. Also you can find our reply to that comment. http://www.ntu.edu.sg/home/ygmu Best regards Yuguang Dr. Yugu

RE: [gmx-users] a question about gmx3.3 replica exchange

>but what is the meaning of " repl pr " ? It means replica exchange probability . >i noticed that when "X" symbol appearing , most of the value of " repl pr" >appoarch 1.0.But in some cases, the value is about 0.2-0.3, also the "X" >symbol appears. >So i don\'t really catch the point about th