Re: [gmx-users] First Principle Component Analysis

Hi, For ED analysis you don't need to run make_edi. Check g_covar and later g_anaeig. Ran. Anirban Ghosh wrote: > Hi All, > I want to do ED analysis along first principle component in GROMACS. I > am trying to make the .edi file through make_edi command. But cannot > understand which option to p

[gmx-users] First Principle Component Analysis

Hi All, I want to do ED analysis along first principle component in GROMACS. I am trying to make the .edi file through make_edi command. But cannot understand which option to pick among -linfix. -linacc, -radfix, -radacc, -radcon. I also cannot understand how to specify the option(string) for th

Re: [gmx-users] infiniband question

Andrei Neamtu wrote: Hello gmx, I have a question regarding infiniband interconnect: Is there any difference (in terms of performance) between integrated on-board infiniband (ex. Mellanox) and PCI-Express infiniband adaptors (due to pci-e limitations)? Which one is recomended. We are in a proces

Re: [gmx-users] Problems using mdrun_d

Arneh Babakhani wrote: sure, here you go, [EMAIL PROTECTED] ~]$ ldd /u1/ababakha/gromacs-3.3.1_double_precision_mpi/bin/mdrun_d libnsl.so.1 => /lib/libnsl.so.1 (0x006e4000) libm.so.6 => /lib/tls/libm.so.6 (0x00ae3000) libXm.so.3 => /usr/X11R6/lib/libXm.so.3 (0x0020c000)

Re: [gmx-users] Problems using mdrun_d

sure, here you go, [EMAIL PROTECTED] ~]$ ldd /u1/ababakha/gromacs-3.3.1_double_precision_mpi/bin/mdrun_d libnsl.so.1 => /lib/libnsl.so.1 (0x006e4000) libm.so.6 => /lib/tls/libm.so.6 (0x00ae3000) libXm.so.3 => /usr/X11R6/lib/libXm.so.3 (0x0020c000) libXt.so.6 => /usr/

Re: [gmx-users] Problems using mdrun_d

this is mostly likely due to mismatched version between runtime library and compile library. Could you run ldd full/path/to/mdrun_d and paste the output here for us to continue our help? On 9/6/2007 5:43 AM, Arneh Babakhani wrote: Hi, I've compiled a mpi double-precision version of mdrun_d.

Re: [gmx-users] Problems using mdrun_d

Arneh Babakhani wrote: Hi, I've compiled a mpi double-precision version of mdrun_d. I'm trying to use it, but I get the following error. Any ideas what the 'symbol lookup error' is? -- [EMAIL PROTECTED] Window-1]$ mpirun -np 4 mdrun_d -np 4 -s UmbrellaMD.tpr -o Umbrell

Re: [gmx-users] How to use PRODRG to help new user do gromacs?

St�phane, Thank you so much. I will try your suggestion. Yafei - Original Message - From: [EMAIL PROTECTED] Date: Wednesday, September 5, 2007 6:22 pm Subject: Re: [gmx-users] How to use PRODRG to help new user do gromacs? > Selon Yafei Dai <[EMAIL PROTECTED]>: > > > Hi, all, > > I am a

Re: [gmx-users] How to use PRODRG to help new user do gromacs?

Selon Yafei Dai <[EMAIL PROTECTED]>: > Hi, all, > I am a new user of gromacs and I read the manual and tutorial but I still get > confused. > I need your help. > > >From PRODRG, I got four *.top files, one *.itp file and three *.PDB files > and some other files. In my system, I don't have any solv

[gmx-users] infiniband question

Hello gmx, I have a question regarding infiniband interconnect: Is there any difference (in terms of performance) between integrated on-board infiniband (ex. Mellanox) and PCI-Express infiniband adaptors (due to pci-e limitations)? Which one is recomended. We are in a process of buying a cluster o

[gmx-users] Problems using mdrun_d

Hi, I've compiled a mpi double-precision version of mdrun_d. I'm trying to use it, but I get the following error. Any ideas what the 'symbol lookup error' is? -- [EMAIL PROTECTED] Window-1]$ mpirun -np 4 mdrun_d -np 4 -s UmbrellaMD.tpr -o UmbrellaMD -c AfterUmbrellaMD

Re: [gmx-users] How to use PRODRG to help new user do gromacs?

What' in the bottom of drgcns.top? On 9/6/2007 2:03 AM, Yafei Dai wrote: Hi, all, I am a new user of gromacs and I read the manual and tutorial but I still get confused. I need your help. >From PRODRG, I got four *.top files, one *.itp file and three *.PDB files and some other files. In my sys

Re: [gmx-users] Correlation Matrix Calculation

Thanks Tsjerk, One other question, regarding the covar.dat file (the covariance matrix that's outputted when using the -ascii flag): I dont' quite understand the format of it. In the manual, it states: "The order of the elements is: x1x1, x1y1, x1z1, x1x2, ..." Does "1" and "2" refer to th

[gmx-users] How to use PRODRG to help new user do gromacs?

Hi, all, I am a new user of gromacs and I read the manual and tutorial but I still get confused. I need your help. >From PRODRG, I got four *.top files, one *.itp file and three *.PDB files and >some other files. In my system, I don't have any solvents, no any waters and >no any ion. I take t

[gmx-users] RF-excl confusion....

Dear community, Thanks for your kind answer, Berk! I am actually trying to understand the "RF-excl" term, which comes from one of your contributions to version 3.3.: http://www.gromacs.org/content/view/18/132/ If you will, I have a couple of perhaps naive questions: 1) 2 sentences appear to be

Re: [gmx-users] Why Total Energy is positive??

Think about what a carbon nanotube isyou can think about it as a rolled up graphene sheet. Graphene is made up entirely of sp2 carbons - which means that the carbons want to reside in a planar arrangement. Rolling the sheet up into a tube requires energy. Your positive energy reflects this. Bob

Re: [gmx-users] Why Total Energy is positive??

> If it is fine, then how can I compare the result with ab inito's? Thanks. Two things: (1) Total and potential energies are only meaningful up to an additive constant. So there is no reason in principle your potential energy (or total energy) should be negative rather than positive. Just think ab

[gmx-users] Re: Why Total Energy is positive??

And the Potential is also positive. I cannot explain this as well. On 9/5/07, uki zhu <[EMAIL PROTECTED]> wrote: > > Hi, gmx-users, > These days I am trying to do some systems about carbon tubes. And I found > Total Energy of the system is positive whether Energy Minimization or MD. > The amount

Re: [gmx-users] Why Total Energy is positive??

Dear David, If it is fine, then how can I compare the result with ab inito's? Thanks. On 9/5/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > > uki zhu wrote: > > Hi, gmx-users, > > These days I am trying to do some systems about carbon tubes. And I > > found Total Energy of the system is posi

Re: [gmx-users] questions about simulation of water/solid interface

Zhou Bo wrote: Hi all, I want to simulate a water/solid interface, like water on a HOPG surface. I have some questions in construction of the system: The system have a two-layer graphite surface (in the bottom of the box) , a 3 nm thickness of water layer on it, and a vacuum region on th

Re: [gmx-users] Why Total Energy is positive??

uki zhu wrote: Hi, gmx-users, These days I am trying to do some systems about carbon tubes. And I found Total Energy of the system is positive whether Energy Minimization or MD. The amount of Total Energy is about E03. For example, "" Step Time Lambda 5

[gmx-users] questions about simulation of water/solid interface

Hi all, I want to simulate a water/solid interface, like water on a HOPG surface. I have some questions in construction of the system: The system have a two-layer graphite surface (in the bottom of the box) , a 3 nm thickness of water layer on it, and a vacuum region on the water. Questio

[gmx-users] Why Total Energy is positive??

Hi, gmx-users, These days I am trying to do some systems about carbon tubes. And I found Total Energy of the system is positive whether Energy Minimization or MD. The amount of Total Energy is about E03. For example, "" Step Time Lambda 50005.0

Re: [gmx-users] psf 2 top

Hi, On Wednesday, 5. September 2007 14:14, andrea carotti wrote: > Hi all, > I've performed my MD simulations using the charmm FF and NAMD (so > pdb,psf and dcd files). Now i would like to use the great GMX analysis > tools. I've successfully converted the dcd file in trr (using catDCD). > Now the

[gmx-users] psf 2 top

Hi all, I've performed my MD simulations using the charmm FF and NAMD (so pdb,psf and dcd files). Now i would like to use the great GMX analysis tools. I've successfully converted the dcd file in trr (using catDCD). Now the next step I'd like to do is the psf to top conversion. I've seen on the vmd

Re: [gmx-users] make_ndx and residue name length

Thanks... I think I'll just get the CVS make_ndx and integrate that into my current CVS copy, rather than try to hunt the different locations down! - Original Message From: Berk Hess <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Wednesday, September 5, 2007 11:22:15 AM Subject: RE:

RE: [gmx-users] make_ndx and residue name length

From: Alan Dodd <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] make_ndx and residue name length Date: Tue, 4 Sep 2007 10:55:07 -0700 (PDT) The maximum permissible residue name length is at least 5 characters long for a tpr or g

[gmx-users] Re: gmx-users Digest, Vol 41, Issue 10: How to run ED with position restrain along first principle, component (Anirban Ghosh)

4. How to run ED with position restrain along first principle component (Anirban Ghosh) You can either keep it fixed with the -linfix option of mk_edi. The other option is to use the flooding code, with a harmonic restraint on the eigenvector. Check the paper Flooding in groma

[gmx-users] How to run ED with position restrain along first principle component

Hi All, I want to do essential dynamics study with position restrain along first principle component. But I don't know how to proceed. Is there any command in GROMACS to do is? Or do I need to manually create any file for doing this? Please tell me how to do this. Regards, Anirban Ghosh