Re: [gmx-users] How to install gromacs 4.5.1

post? Read http://www.gromacs.org/Support/Mailing_Lists -- Best Regards, lina -- 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

Re: [gmx-users] how to calculate the conc in the genion

On Thu, Aug 11, 2011 at 10:41 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 12/08/2011 12:37 AM, lina wrote: Hi, after using genion -conc 0.1 certain number of Na and Cl were added in solvent. but when I tried to calculate back, namely, based on the number of Na and Cl, the number

Re: [gmx-users] how to calculate the conc in the genion

to the local concentration you might need to use? Solutes, membranes and voids may alter the local concentration significantly. By the way, Lina, it would have helped if you had given the equations, numbers and outcomes that lead you to believe there is something wrong. I did another quick check

Re: [gmx-users] how to calculate the conc in the genion

the water, certainly the water volumn will be greatly smaller than the box volumn, so the concentration will reach very high? I might be wrong in some way, hope someone can point out. Thanks, By the way, Lina, it would have helped if you had given the equations, numbers and outcomes that lead you

Re: [gmx-users] how to calculate the conc in the genion

On Fri, Aug 12, 2011 at 8:08 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 12/08/2011 2:22 AM, lina wrote: On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaartsje...@gmail.com  wrote: Hi, I'd be amazed if the error was in the code and not in your calculation. The number of water

Re: [gmx-users] How to run solvation dynamics for some organic molecules

don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

Re: [gmx-users] Regarding Segmentation fault during mdrun_d

, lina -- 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 www interface or send it to gmx

Re: [gmx-users] bug in editconf for making a box ? combined two residues into one

, lina -- 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 www interface or send it to gmx

[gmx-users] How to examine the problem of one atom during EM

= 2.89751132744731e+04 on atom 8524 Norm of force = 2.18622026854678e+02 Thanks for any advice, -- Best Regards, lina -- 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

Re: [gmx-users] How to examine the problem of one atom during EM

On Wed, Jul 27, 2011 at 7:29 PM, Justin A. Lemkul jalem...@vt.edu wrote: lina wrote: Hi, Form the begining to 5 steps, during EM, all exit in atom 8524, how do I check it further? I mean, from which parts to examine? I also switched to double version to run the EM. Open your

Re: [gmx-users] How to examine the problem of one atom during EM

On Wed, Jul 27, 2011 at 9:06 PM, Justin A. Lemkul jalem...@vt.edu wrote: lina wrote: On Wed, Jul 27, 2011 at 7:29 PM, Justin A. Lemkul jalem...@vt.edu wrote: lina wrote: Hi, Form the begining to 5 steps, during EM, all exit in atom 8524, how do I check it further? I mean, from

Re: [gmx-users] Weird problem

/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Gromacs on IBM clusters

)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] restarting stopped mdrun

-- Best Regards, lina -- 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 www

Re: [gmx-users] help on mdrun

to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] Mopac/Gmx QMMM

/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users

Re: [gmx-users] g_hbond/g_sas - how is it calculated?

! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

Re: [gmx-users] binaries for mac os x 10.6

/Support/Mailing_Lists -- Best Regards, lina -- 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

Re: [gmx-users] hi

On May 29, 2011, at 20:45, rashi.pari...@gmail.com wrote: Hi all.. I want to ask if it is possible to restart the md run if due to power problem final md run not completed means initiating md from where is stop due to any reason? Suppose your .tpr is topol.tpr mdrun -cpi state.cpt Or

Re: [gmx-users] about g_hbond

I got it. I should have outputted the -hbn file. Thanks, On Thu, May 12, 2011 at 1:09 PM, lina lina.lastn...@gmail.com wrote: /* y-label: Hydrogen Bond Index */ is it relevant to the total number of hydrogen bonds? such as /* XPM */ /* x-label: Time (ps) */ /* y-label: Hydrogen Bond

Re: [gmx-users] index file

! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] index file

2011/5/12 Justin A. Lemkul jalem...@vt.edu: lina wrote: make_ndx -f your.gro/pdb -n your.ndx -o your.ndx LiGA LİGB: This is not correct.  You need to use | rather than .  Using logical and () means the index group will contain atoms that are common to both LIGA and LIGB

[gmx-users] about g_hbond

Hi, For group A, b, C. It's no doubt can get hb forming number between A-b, b-C. b-(A or C). But I don't know how to get the number of residues of b forming both with A and B at the same time. namely b-AC, not with AC group. Thanks, -- Best Regards, lina -- Best Regards, lina -- gmx

Re: [gmx-users] about g_hbond

, 2011 at 11:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: lina wrote: Hi, For group A, b, C. It's no doubt can get hb forming number between A-b, b-C. b-(A or C). But I don't know how to get the number of residues of b forming both with A and B at the same time. namely b-AC, not with AC

Re: [gmx-users] amber force field

In latest version of gromacs (4.5.4 or earlier) The amber force fields were provided. -- Best Regards, lina -- 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

Re: [gmx-users] openmm 3.0, opencl support

Have you installed the CUDA Toolkit 4.0 ? I have never tried, just guessed. lina On Mon, Apr 25, 2011 at 9:17 AM, Claus Valka lastexile...@yahoo.de wrote: Hello, I'm interested in knowing the level of development about gromacs supporting the opencl framework language. I have read

Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?

There is another free tool (Avogadro) which is pretty easy to handle this also. Try http://avogadro.openmolecules.net/wiki/Get_Avogadro in Build -- Inert --- Peptides, Which is very easy to use. you can choose Straight line, beta sheet or alpha helix or other. and save as .pdb lina -- gmx

Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?

apt-get install avogadro http://avogadro.openmolecules.net/wiki/Distribution_Packages On Wed, Apr 20, 2011 at 10:34 PM, ZHAO Lina lnzha...@gmail.com wrote: There is another free tool (Avogadro) which is pretty easy to handle this also. Try http://avogadro.openmolecules.net/wiki

Re: [gmx-users] drawing the plots

xmgrace gyrate.xvg On Sat, Apr 16, 2011 at 2:09 PM, Sajad Ahrari sajadahr...@yahoo.com wrote: hello dear Gromacs users i have Gromacs4.5.3 installed on suse11.1.but when i run commands like g_gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg i can't see any plot drawn. although the

Re: [gmx-users] Installation error

You are really PATIENT waiting for FOUR months for the answers. Ask the person around you they might be able to provide useful suggestions. There might be some libs linking problem. I have never tried the Cygwin, you may really try searching first before waiting. lina P.S if I were you, I

[gmx-users] make_ndx

is wrong. if use a C11 ri 1-100, the atom is 100, which is right. I want to know how can I use ! to exclude some group? This mistake is reproducible and I didn't figure it out (Even I examined the .gro). Thanks for any suggestion. lina -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Re: make_ndx

such as residue 288 which is has C when I tried a C, it's inclusive residue 288. while tried the ri 288 a C, it showed me Group is empty. Thanks, On Sun, Mar 27, 2011 at 1:42 PM, ZHAO Lina lnzha...@gmail.com wrote: Hi, Does the ! in make_ndx work? | and work, but seems ! not work. I

Re: [gmx-users] Re: g_hbond output

the cutoff distance, but beyond the cutoff angle. You may got different number of hbonds using different cutoff distance and cutoff angle. Jianguo -- *From:* ZHAO Lina lnzha...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, 16

[gmx-users] g_hbond output

@ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2 1000 1 0 :

[gmx-users] Re: g_hbond output

realization it sent. lina -- 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 www interface

Re: [gmx-users] terminated but not completely

-cpi state.cpt -append try to add those two options at the end of your mdrun lina On Sun, Mar 13, 2011 at 5:53 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear All I run a simulation for 4 days. Unfortunately it terminated,but not completely,1 steps from 2 has

[gmx-users] secondary structure propensities of residues

Hi, How do get the percentage of the secondary structure propensities of residues? seems dssp none such effect? Thanks for any answers. lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] select in pymol after trjconv

tried the select protein, resi 1-48 some waters are inclusive. Thanks for any suggestion. lina -- 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] select in pymol after trjconv

On Mon, Mar 7, 2011 at 10:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: ZHAO Lina wrote: Hi, after added ions, I got a solv_ions.gro. I use trjconv to produce the solv_ions.pdb when I view it in pymol. I showed sequence, it like 1 2 3 4 6 ODOAOEOROHODOGOOYE

Re: [gmx-users] select in pymol after trjconv

with pymol) Thanks again, lina -- 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 www

Re: [gmx-users] select in pymol after trjconv

. genconf works so perfect here. Thanks again! lina -Justin Thanks again, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu

[gmx-users] where does the gromacs looks for the top data file.

for top data files in ~/share After in topol.top I put ; Include forcefield parameters #include /home/lina/share/gromacs/top/gromos43a1.ff/forcefield.itp I still have following problems. Program grompp, VERSION 4.5.3 Source code file: futil.c, line: 897 Fatal error: Library file residuetypes.dat

Re: [gmx-users] where does the gromacs looks for the top data file.

On Mon, Mar 7, 2011 at 11:11 PM, Justin A. Lemkul jalem...@vt.edu wrote: ZHAO Lina wrote: Hi, I got another question about where does the gromacs looks for the top data file. Specifically, The ~/bin ~/lib and ~/share are under my home directory. the general setting (in .bash_profile

Re: [gmx-users] Gromacs Installation

directory and install. 2] a better but a bit not so-easy way, is download the source ( http://packages.debian.org/sid/gromacs), built the package and add it into repository. There maybe also some other ways. HTH, lina On Tue, Feb 15, 2011 at 6:23 AM, majid hasan pu_majidha...@yahoo.comwrote: Dear

Re: [gmx-users] Gromacs Installation

You are right, it's relevant to the shared libs. but I don't know why you failed in the second attempt if you did a clean reinstallation. lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Re: [gmx-users] Gromacs Installation

clean reinstallation. make uninstall make distclean rm -r the untar one from source re-install it again. lina On Tue, Feb 15, 2011 at 12:39 PM, majid hasan pu_majidha...@yahoo.comwrote: Okay. Actually, second time, I over-worte the first installation. I mean I didn't uninstall the first one

Re: [gmx-users] add force field

I do believe so. ^_^ it works beautifully with the newly-added force field. Thanks, lina On Wed, Feb 9, 2011 at 5:11 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/02/2011 7:47 PM, lina zhao wrote: Hi, it works before I thought it might share some similarity with 4.0.7 which some

[gmx-users] add force field

Hi, Anyone has successfully tried to add some new force field in the default force field (in 4.5) so pdb2gmx can show up the (newly-added) force field which will also be recognized by gromacs, Thanks, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] dssp problem

http://biskit.pasteur.fr/install/applications/dssp wget ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip unzip dsspcmbi.zip cd dssp ./DsspCompileGCC cd .. sudo mv dssp /usr/local/src/ cd /usr/local/bin sudo ln -s ../src/dssp/dsspcmbi . lina On Sat, Dec 25, 2010 at 8:45 PM, Mark

RE: [gmx-users] find the relevant structure out

might make something wrong cause I did it really clumsily. Thanks for your answering, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Wednesday, November 24, 2010 3:19 PM

RE: [gmx-users] find the relevant structure out

, when I tried alter in pymol to show the beat-sheet as the way Justine mentioned in early email, it's really look weird. I noticed lots of paper they use DSSP to say something. Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun

RE: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

I just tried the same way as using NA+, by genion -s ions.tpr -o protein_solvated_ions.gro -p topol.top -pname K+ -nname CL- -np Number_of_K It works, u may do a try. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf

RE: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

When I went a bit further, I found it's wrong. Sorry. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of #ZHAO LINA# [zhao0...@e.ntu.edu.sg] Sent: Monday, November 22, 2010 4:50 PM To: Discussion list for GROMACS users Subject: RE

RE: [gmx-users] find the relevant structure out

I really do not know how to get those beta-sheet structures out, or maybe by which ways? Any clues are warmly welcomed and appreciated. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au

[gmx-users] find the relevant structure out

thought might be representive, but under pymol, show cartoon, there is none beta sheet at all. There were 5000 frames, I really do not know which one is most representive. Or maybe some parts I understand wrong. Thanks for any advice and if I am wrong please let me know, lina -- gmx-users

RE: [gmx-users] find the relevant structure out

the way from you are looking at the wrong files, to pymol's definition of a beta sheet doesn't agree with dssp. what are those files I should have looked for, and how could I find a better way to show those beta-sheet out? Thanks, lina From: gmx-users-boun

[gmx-users] noxvgr

Hi, Suppose when I use gyrate, I want the output to be the eps, when I tried -noxvgr -w sounds I failed to get. I do not understand it well. I can get .xvg picture, and seems the gnuplot not easy to interpret and save it as .eps or png. Any idea? Thanks and best, lina -- gmx-users

RE: [gmx-users] noxvgr

I suspect it might mine grace was wrong, when I tried to use save as, it has bugs, I will check this first. Thanks for your answering. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu

RE: [gmx-users] noxvgr

It works (cool). Thanks for both of you. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 19, 2010 10:23 PM To: Discussion list for GROMACS users Subject: Re

RE: [gmx-users] DSSP error

http://biskit.pasteur.fr/install/applications/dssp http://oldwww.gromacs.org/pipermail/gmx-users/2009-April/041004.html http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp?highlight=dssp HTH, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun

RE: [gmx-users] which force file has parameters for creatine md simulations

http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Olga Ivchenko [olga.ivche...@gmail.com] Sent: Friday, November 05, 2010 6:02 PM To: gmx-users@gromacs.org Subject: [gmx

[gmx-users] dssp

try dssp, so do not know how to examine it. Thanks for any advice, lina -- 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

RE: [gmx-users] dssp

Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina

RE: [gmx-users] dssp

I did choose 1 protein when it asked me to choose. Thanks for your answering, I may try on my desktop another time. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Linus Östberg [bio...@talavis.eu] Sent: Friday

RE: [gmx-users] dssp

Hi, 1. There is no wrong in mine executable path, it's mine fault that I MODIFIED the real and true path to a simple way as it showed pathTo... before I posted. 2. seems not about root things, cause every body can write and read to/from /dev/null 3. I will try another time ?! Thanks, lina

RE: [gmx-users] dssp

to execute command: /home/src/DSSP/ -na ddCFya2b ddJZ2M0k /dev/null 2 /dev/null was something wrong with mine DSSP, except path reason. Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of #ZHAO LINA# [zhao0

RE: [gmx-users] dssp

Last email the paths really look messy, because as I said before, I modified by mine hand before posted it. Sorry about that. I did export the path before. :-) Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf

[gmx-users] mirror reflection

Hi, which can help to get the mirror reflection of a known protein? Thanks, lina -- 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] mirror reflection

users Subject: Re: [gmx-users] mirror reflection editconf -scale -1 -1 -1 On Tue, Oct 26, 2010 at 12:56 PM, Erik Marklund er...@xray.bmc.uu.se wrote: #ZHAO LINA# skrev 2010-10-26 11.46: Hi, which can help to get the mirror reflection of a known protein? Thanks, lina If it's just one

RE: [gmx-users] mirror reflection

I got. -rotate. sorry and thanks. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of #ZHAO LINA# [zhao0...@e.ntu.edu.sg] Sent: Tuesday, October 26, 2010 8:47 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users

RE: [gmx-users] Re: published paper related to protein simulation, using gromacs

Hi, I think, started from some gromacs tutorial is a nice ideas and then during those process you certainly will meet some paper. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Thomas Schlesier [schl...@uni

[gmx-users] position_restraints

section to the right molecule. Thanks for any clue. The part belongs to the one I want to restraints. I mean, the molecule is right. Thanks, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Intrinsically disordered proteins

, is it acceptable to just take one, say model 1? Thanks for any answering, lina -- 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

RE: [gmx-users] Intrinsically disordered proteins

/modules can be put ? I tried the put the packmolextension.so under usr/lib/avogadro/1_0/extensions/ but seems not work, Might someone has tried and knew the answer, actually I had asked on the other place, but none feedback. 2. Wow, it's going to be lots of works. lina

[gmx-users] How can I best setup the nodes number

to hopefully run quickly. Thanks and best regards, lina -- 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

RE: [gmx-users] How can I best setup the nodes number

I think I know how many ppn one nodes have. :-) My question was that the number of ppn has something to do with the PME mesh part number or not? Why sometimes I had a big load imbalance. Thanks and best regards, lina From: gmx-users-boun...@gromacs.org [gmx

RE: [gmx-users] Re : installation of gromacs in windows on cygwin

sudo apt-get install grace From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, October 06, 2010 11:29 AM To: Gromacs Users' List Subject: Re: [gmx-users] Re : installation of

[gmx-users] protein embedded into membrane.

). or, Can we locally inflated those membrane and then locally packed them together. Very local, or maybe just simply removed those lipids. How could I make sure the removal ones are going to be nice, from which sides I should check. Thanks and best regards, lina p.s To avoid a very trivial

RE: [gmx-users] protein embedded into membrane.

regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, October 04, 2010 11:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] protein embedded

[gmx-users] cholesterol

Hi, Are there some tutorials handling the cholesterol stuff. I read several literature but choked in some places. Thanks with best regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

RE: [gmx-users] cholesterol

much in those specific simulations yet, just beginning stage. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, October 01, 2010 8:35 PM To: Discussion list for GROMACS

RE: [gmx-users] cholesterol

Hi, Thanks for your answer, I will spend some time to figure it out. By the way, any links or literature or something relevant to it warmly welcome to introduce them to me. Best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun

RE: [gmx-users] cholesterol

Thanks for your clue. I found the very interesting paper about that force field. Thanks again, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Thomas Piggot [t.pig...@soton.ac.uk] Sent: Friday, October 01, 2010 9

[gmx-users] lipids number

dppc128 ones. Thanks and best regards, lina -- 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

RE: [gmx-users] lipids number

I have a vague impression about that, seems someone asked similar things before. I will do a try and see. Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday

RE: [gmx-users] Getting started - Peptide

Are you sure you installed the version 4.0.7? Hint : your program run on VERSION 4.5.1, Answer : You know. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Artur Panczakiewicz [apanczakiew...@gmail.com] Sent

[gmx-users] Position Restraints

Hi, When I used the genrestr to get the posre.itp specially, I found it set all atom to be applied to. Is that okay? How could I figure out which ones should not be set to. A little naive questions, but I do do not know. Thanks with regards, lina -- gmx-users mailing listgmx-users

RE: [gmx-users] Position Restraints

Thanks for your answer. How can I tell which ones I should restrain? all no-H atoms? in most general situations. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday

RE: [gmx-users] Position Restraints

Thanks for your answer again. I will restrain the heavy atoms only first. Best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, September 22, 2010 11:43 AM

[gmx-users] top directory can be split or not?

Hi, Just curious, whether the top directory can be split like: /usr/share/gromacs/top /usr/local/share/gromacs/top $HOME/share/gromacs/top Thanks, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] how to let the grompp finding library from working directory first.

--- Do I need add something in minim.mdp? Or maybe just some parts wrong I do not realise. Thanks and best regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

RE: [gmx-users] how to let the grompp finding library from workingdirectory first.

Yes. I did it already. But it did not work. in topol.top file, ;Include topology #include HO.itp Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Dallas Warren [dallas.war...@monash.edu] Sent: Tuesday, September 14

RE: [gmx-users] how to let the grompp finding library fromworkingdirectory first.

The HO.itp is nothing wrong with this. I found the answer from last part of this page (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html). It's a bit trivial and I will test it later. Thanks again for you time. lina

RE: [gmx-users] Need help!!!

Make sure your gromacs is the latest version. If not, update and try again. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of praba vathy [sumipraba2...@gmail.com] Sent: Thursday, September 02, 2010 9:06 PM To:

RE: [gmx-users] Need help!!!

But it's a bit trivial to modify those things if you just following those steps by steps. Using the latest version can save lots of works. By the way, thanks for the website, I once followed that too (nearly step by step also). Thanks with best regards, lina P.S actually you can upgrade your

RE: [gmx-users] g_covar

YourSourceCode/gromacs/src/tools/ If in Linux OS, try locate g_covar.c p.s 4.0.3 is not the latest version. why do not try the latest version? From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Carla Jamous

RE: [gmx-users] How to calculate the distances

Dear Mark, It works. Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, August 26, 2010 1:48 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] How

[gmx-users] How to calculate the distances

. Thanks, lina -- 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 (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ

[gmx-users] the mdrun choked or maybe braked.

. Thanks for any advice, lina -- 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 (un)subscribe requests to the list. Use the www interface or send

RE: [gmx-users] the mdrun choked or maybe braked.

. #ZHAO LINA# wrote: Hi, The problem just like this, in md.log There are: 130889 Atoms splitting topology... Walking down the molecule graph to make constraint-blocks

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