[gmx-users] Re: Umbrella sampling with large pulling distance (larger than half of the box size) (Thomas Schlesier)

-- Message: 1 Date: Wed, 20 Mar 2013 12:55:45 +0100 From: Thomas Schlesier schl...@uni-mainz.de Subject: [gmx-users] Umbrella sampling with large pulling distance (larger than half of the box size) To:

[gmx-users] why Blue Gene/Q is so slow?

Dear all, I am running a 9000 atom system with GBSA (Gromacs 4.5.5) in a Blue Gene/Q cluster. I got the speed 1.002 ns/day with 8 cores. However, in my own workstation with 8 cores the same system can reach nearly 10 ns/day (Intel(R) Xeon(R) CPU E5620 @ 2.40GHz). Can anyone tell me what's

[gmx-users] Re: Re: why Blue Gene/Q is so slow? (Mark Abraham)

/plain; charset=ISO-8859-1; format=flowed On 17/07/2012 5:00 PM, DeChang Li wrote: Dear all, I am running a 9000 atom system with GBSA (Gromacs 4.5.5) in a Blue Gene/Q cluster. I got the speed 1.002 ns/day with 8 cores. However, in my own workstation with 8 cores the same system can reach

[gmx-users] Free energy calculation about ions (hope Justin A. Lemkul can give some suggestions )

at all. Does this affact my calculation? = Dechang Li , Ph.D Biomechanics and Biomaterials Laboratory Department of Applied Mechanics School of Aerospace Engineering Beijing Institute of Technology Beijing 100081, P. R. China

[gmx-users] Can Gromacs do Targeted MD simulation?

Hi all, Just as the title, can Gromacs do Targeted MD simulations? If Yes, how to set up the simulation procedure? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] How to exclude the interactions between molecule A and B in Gromacs?

) between some small molecules (e.g. ligand A and its replica). How can Gromacs to do this? Any suggestion will be very appreciated. Best regards, = Dechang Li, Ph.D Biomechanics and Biomaterials Laboratory Department of Applied Mechanics School of Aerospace

[gmx-users] distance VS. direction option in Umbrella sampling, in Gromacs 4.0

Dear all, What is the difference between the option Distance and Direction in Umbrella Sampling? In my opinion, the option Direction means that pulling the pull_group1 through the direction related to the reference group. Right? But how about the option Distance? -- gmx-users mailing

[gmx-users] Re: distance VS. direction option in Umbrella sampling, in Gromacs 4.0 (Justin A. Lemkul)

Message-ID: 4ce280b6.2080...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed DeChang Li wrote: Dear all, What is the difference between the option Distance and Direction in Umbrella Sampling? In my opinion, the option Direction means that pulling

[gmx-users] Umbrella sampling with temperature and pressure coupling method problem

Dear all, I want to use umbrella sampling to calculate the PMF of the conformational transition of a protein. What temperature coupling method and pressure coupling method should I use? Berendsen temperature coupling or Nose-Hoover temperature coupling? Or each one is OK? -- gmx-users

[gmx-users] Re: Umbrella sampling with temperature and pressure coupling method problem (Justin A. Lemkul)

Message: 6 Date: Tue, 19 Oct 2010 09:30:47 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Umbrella sampling with temperature and pressurecoupling method problem To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID:

[gmx-users] Re: Re: Umbrella sampling with temperature and pressure coupling method problem (Justin A. Lemkul) (Justin A. Lemkul)

Message-ID: 4cbdd022.6020...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed DeChang Li wrote: Message: 6 Date: Tue, 19 Oct 2010 09:30:47 -0400 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] Umbrella sampling

[gmx-users] about the option pull_dim

Dear all, Does the following three options do the same things in the pull code of Gromacs 4.0: 1. pull_dim = Y Y Y pull_vec1 = 1 0 0 ** 2. pull_dim = Y N N pull_vec1 = 1 0 0 ** 3. pull_dim = Y N N pull_vec1 = 1 0.5 0.5 -- gmx-users

[gmx-users] what is the eigenvalue unit in Gromacs?

Dear all, I used g_nmeig to diagonalize the Hessian matrix, that I got the eigenvalues. However, I found that in the file 'eigenval.xvg' the unit of the eigenvalues are Eigenvalue [Gromacs units]. What is the '[Gromacs units]'? -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] the code speed between Gromacs 3.0 and Gromacs 4.0

Dear gmx-users, Are there any comparisons of the code speed between Gromacs 3.0 and Gromacs 4.0. In my calculation, I got a speed about 3.5ns/day of a system have about 50,000 atoms, using 8 CPUs with Gromacs 3.3.1. In contrast, the speed can reach up to 7.3ns/day when switch to

[gmx-users] How to calculate the lifetime of one hydrogen bond

? Best regards, 2009-1030 = Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China Tel: +86-10-62773574(O) Email: lid...@mails.tsinghua.edu.cn

[gmx-users] Different RMSD of the same system

24.0190.1102782 26.0190.1115073 28.0190.1304575 30.0190.1173159 Best regards, = Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China Tel: +86-10-62773574(O

[gmx-users] Re: force field parameter for ligands

Message: 1 Date: Mon, 25 May 2009 01:15:44 -0700 From: Zhanglin Ni z...@u.washington.edu Subject: [gmx-users] force field parameter for ligands To: gmx-users@gromacs.org Message-ID: 009701c9dd11$012c1ae0$0301a...@zn3 Content-Type: text/plain; format=flowed; charset=iso-8859-1;

[gmx-users] the vdw and electrostatic energy

, = Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China Tel: +86-10-62773574(O) Email: lidc02 at mails.tsinghua.edu.cn = ___ gmx-users mailing listgmx

[gmx-users] Re:Re: the vdw and electrostatic energy (Ran Friedman)

the energy from the file ener.edr, does the cutoff affect the values of the energy? For example, when the cutoff is set to 1.2 nm and the PME method is used, does the energy term Coul-SR read by g_energy contain the long range part ? Ran. Dechang Li wrote: Dear all, When we do a MD simulation

[gmx-users] How VMD to display the velocity

be displayed by the arrowhead and the length of the arrows? If NO, how can I do this work with other package? Thanks in advance! Best regards, 2009-3-5 = Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China

[gmx-users] eigenvec.trr and eigenval.xvg

= Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China Tel: +86-10-62773574(O) Email: lid...@mails.tsinghua.edu.cn

[gmx-users] generalized order parameters S2

to a reference strucutre firstly, and then calculate S2 using command 'g_rotacf'? If YES, what the reference structure is? The average structure in the trajectory? Best regards, 2009-3-3 = Dechang Li, Ph.D Candidate Department of Engineering Mechanics

[gmx-users] g_rotacf, order parameter S2 problem

= Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773574(O) Email: lid...@mails.tsinghua.edu.cn = ___ gmx-users mailing list

[gmx-users] Re: Re: calculation of the order parameter S2 (Xavier Periole)

Dechang Li wrote: Dear all, I want to use g_rotacf to calculate the order parameter(S2, N-H bond in main chian). The tool g_rotacf needs an index.ndx file that contains two vectors. g_rotacf wants the index number of two atoms to calculate the order parameter of an NH vector

[gmx-users] Re: Re: calculation of the order parameter S2 (Xavier Periole)

=flowed On Sun, 04 Jan 2009 13:38:33 +1100 Mark Abraham mark.abra...@anu.edu.au wrote: Dechang Li wrote: Dear all, I want to use g_rotacf to calculate the order parameter(S2, N-H bond in main chian). The tool g_rotacf needs an index.ndx file that contains two vectors. g_rotacf wants

[gmx-users] S2Min and S2Max

, 2009-1-3 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: li.d...@gmail.com

[gmx-users] calculation of the order parameter S2

regards, 2009-1-4 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: li.d...@gmail.com

[gmx-users] questions about g_hbond

column? Best regards, = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED

[gmx-users] system contains proteins and DNAs with ffamber99

ffamber99 to simulate the system which contains proteins and DNAs? Best regards, = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED

Re: [gmx-users] g_hbond distance distribution problem

;charset=utf-8;format=flowed Dechang Li wrote: Dear all, I used command g_hbond to calculated the distance distribution of hbonds in my system. There are two columns in the file hbdist.xvg, as showed follow: @title Hydrogen Bond Distribution @xaxis label Hydrogen

[gmx-users] g_hbond distance distribution problem

= Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] = ___ gmx-users

[gmx-users] Re: the number of water molecules (Jian Zou)

about 5 angstrom? Is that possible in Gromacs? Best regards, 2008-4-20 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED

[gmx-users] the number of water molecules

Dear all, How can I calculate the number of water molecules around the protein with a distance about 5 angstrom? Is that possible in Gromacs? Best regards, 2008-4-20 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua

[gmx-users] Re: Re: RMSD VS. parallel simulation (Mark Abraham)

gmx-users-request,您好！ Message: 1 Date: Sat, 5 Apr 2008 11:48:15 +0800 From: DeChang Li [EMAIL PROTECTED] Subject: [gmx-users] RMSD VS. parallel simulation To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Dear all, I

[gmx-users] Re: RMSD VS. parallel simulation

the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. RMSD VS. parallel simulation (DeChang Li) 2. Re: RMSD VS. parallel simulation (Mark Abraham

[gmx-users] RMSD VS. parallel simulation

simulation, the RMSD of protein at t=0 was about 0.1 nm, why not equal to zero? I used the initial structure for the least squares fit. Best regards, 2008-4-5 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing

[gmx-users] different results when using different number cpus

= Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED] =　 ___ gmx-users mailing

[gmx-users] Grid: 19 x 14 x 14 cells

, 2007-12-2 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED

[gmx-users] Incomplete header: nr 3078 time 9408

resolve it? Best regards, 2007-11-11 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED

[gmx-users] Re:Re: Incomplete header: nr 3078 time 9408

@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=UTF-8; format=flowed Dechang Li wrote: Dear all, I used Gromacs-3.3.1 to do a simulation. When it finished, I used command g_dist to calculate two groups distance VS time. But at time 9408ps, it stopped and showed

[gmx-users] g_hbond

- | H Best regards, 2007-10-17 = Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED

[gmx-users] Amber to Gromacs

, another one is the script. They are in a compressed file in the attached. The command used may be: ./amb2gmx.pl --prmtop XK.prmtop --crd XK.prmcrd --outname XK Best regards, 2007-10-13 = Dechang Li, PhD

[gmx-users] ANTECHAMBER GAFF

= Dechang Li, PhD Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 PR China Tel: +86-10-62773779(O) Email: [EMAIL PROTECTED

[gmx-users] Re: ANTECHAMBER GAFF

replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Gromacs for Aerosol Particle Agglomeration (Lorenzo Isella) 2. Re: Gromacs for Aerosol Particle Agglomeration (Yang Ye) 3. ANTECHAMBER GAFF (Dechang Li) 4. Re

[gmx-users] Large VCM problems

= 0.2 tc-grps = protein ref_t = 300.0 Thank you for your answers. Dechang Li [EMAIL PROTECTED] 　　2007-04-16 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx

[gmx-users] Twin-range neighbour searching (NS) with simple NS algorithm not implemented

hi, Can anyone tell me what does this error mean? ERROR: Twin-range neighbour searching (NS) with simple NS algorithm not implemented my md.mdp file was set: ns_type = grid pbc = xyz Thank you very much! Li,DC Department of Engineering Mechanics Tsinghua University Beijing