[gmx-users] Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for

Dear gmx-users: When I try to simulation a system: protein + ligand molecule using the Implicit Solvent method. the parameters of Ligand were produced by acpype, but when grompped, the appeared" " Velocities were taken from a Maxwell distribution at 300 K GB parameter(s) missing or negative for

[gmx-users] Atomtype 1

Dear gmx-users:   I add a new residue in *rtp ,according to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, and modified corresponding files :such as atp, hdb , after making a full copy of the installed forcefield in woring diectory. When pdb2gmx_d   appeared "  

Re: [gmx-users] Atomtype 1

in fact, the program  hang. --- 12年6月3日，周日, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] Atomtype 1 收件人: "Discussion list for GROMACS users" 日期: 2012年6月3日,周日,下午8:46 On 6/3/12 8:24 AM, xi zhao wrote: > Dear gmx-users: > I add a new residue in *r

Re: [gmx-users] Atomtype 1

: [gmx-users] Atomtype 1 收件人: "Discussion list for GROMACS users" 日期: 2012年6月3日,周日,下午8:46 On 6/3/12 8:24 AM, xi zhao wrote: > Dear gmx-users: > I add a new residue in *rtp ,according to > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, > and

Re: [gmx-users] Atomtype 1

月3日,周日,下午8:46 On 6/3/12 8:24 AM, xi zhao wrote: > Dear gmx-users: > I add a new residue in *rtp ,according to > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, > and modified corresponding files :such as atp, hdb , after making a full copy > of >

Re: [gmx-users] Atomtype 1

in windows , I use ultraedit, in linux ,use vi --- 12年6月3日，周日, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] Atomtype 1 收件人: "Discussion list for GROMACS users" 日期: 2012年6月3日,周日,下午9:19 On 6/3/12 9:16 AM, xi zhao wrote: > > I use Ultraedit to prod

Re: [gmx-users] Atomtype 1

OK, we find the bug. several words have problem of Uppercase and lowercase. thank you very much! --- 12年6月3日，周日, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] Atomtype 1 收件人: "Discussion list for GROMACS users" 日期: 2012年6月3日,周日,下午9:19 On 6/3/12 9:16 AM, xi

[gmx-users] how to build a mixed lipid bilayer?

Dear Users: I would like to build a mixed lipid bilayer (POPE/POPG=3:1) in the MD using Gromacs, please provide some tools for producing the structures or existing structures (PDB or gro files).     Thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.or

Re: [gmx-users] how to build a mixed lipid bilayer?

t; field, you can download the itp and pdb files from > http://www.softsimu.net/downloads.shtml > > If you want CHARMM36, I can send you the files. > > -Jianguo > > > > From: xi zhao > To: gmx-users@gromacs.org > > Sent: Sunday

[gmx-users] how to build xtc file from many same crystal structures which are different conformational states.

Dear gmx-users： I want to analysis PCA for many crystal strcutures, comparing with MD trajectories, but how to build xtc file from many same structures whchi are different conforamtional states. thank you best regards! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromac

[gmx-users] orca and qm/mm

Dear all users: According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and  BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFO file: ! RKS B3LYP/

[gmx-users] orca and qm/mm

All users:   According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and  BASENAME.ORCAINFO as told in the instruction. BASENAME=pyp_qm here is the BASENAME.ORCAINFO file: ! RKS B3LYP/G

回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)

elp' to >     gmx-users-requ...@gromacs.org > > You can reach the person managing the list at >     gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-

回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)

in addition, how to write ORCAINFO?  Is my file right? ! RKS B3LYP/G SV(P) TightSCF Opt  or  RKS B3LYP/G SV(P) TightSCF Opt  --- 11年11月7日，周一, Gerrit Groenhof 写道： 发件人: Gerrit Groenhof 主题: [gmx-users] Re 1. orca and qm/mm (xi zhao) 收件人: gmx-users@gromacs.org 日期: 2011年11月7日,周一,下午9:23 Try

Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)

a question raised:  how to deal with LA in the QMatoms in orca inputfile? using DA ( dummy atom in the ORCA) repaces LA in the QMatoms in the gromacs ? please give me a suggestion! Thank you! --- 11年11月7日，周一, Micha Ben Achim Kunze 写道： 发件人: Micha Ben Achim Kunze 主题: Re: 回复： [gmx-users] Re

Re: 回复： [gmx-users] Re 1. orca and qm/mm (xi zhao)

-- Program mdrun_p, VERSION 4.5.3 Source code file: qm_orca.c, line: 409 Fatal error: Call to '/home/user/orca_x86_64_exe_r2131/orca pyp_qm   how to write the  BASENAME.ORCAINFO? how to deal with LA ?  --- 11年11月8日，周二, Micha Ben Achim Kunze 写道： 发件人: Micha Ben Achim Kunze 主题: Re: 回复： [gmx-us

[gmx-users] ORCA and dummy atom in the gromacs

According to http://wwwuser.gwdg.de/~ggroenh/qmmm.html#code, I want to build qm/mm calculation by using gromacs 4.5.3 + orca 2.8.0. I set up the BASENAME, ORCA_PATH and  BASENAME.ORCAINFO as told in the instruction. When BASENAME.ORCAINFO has no coordinates of QMatoms, the mdrun showns " Back

回复： [gmx-users] Re: 6. ORCA and dummy atom in the gromacs (xi zhao)

t Groenhof 写道： 发件人: Gerrit Groenhof 主题: [gmx-users] Re: 6. ORCA and dummy atom in the gromacs (xi zhao) 收件人: gmx-users@gromacs.org 日期: 2011年11月9日,周三,下午3:30 Did you run also your QM subsystem with the stand-alone version of Orca? >     6. ORCA and dummy atom in the gromacs (xi zhao) >

[gmx-users] orca question and LA

Dear Sir:   How to write a correct BASENAME.ORCAINFO file? According to the instruction “In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given.” It means that BASENAME.ORCAINFO may not contain coordinates of QMatoms part, but when groamcs-ORCA runs , it

Re: [gmx-users] orca question and LA

includes. Again, you should go through Gerrit's tutorials, they should get you going. There are also instructions on how to set up LAs for different force fields. Cheers, Micha On 10/11/11 01:19, xi zhao wrote: Dear Sir:   How to write a correct BASENAME.ORCAINFO file? According t

Re: [gmx-users] orca question and LA

l yet (using cp2k atm). Maybe someone else can advise you. Cheers, Micha On 10/11/11 10:49, xi zhao wrote: I install gmx : ./configure --without-qmmm-orca --without-qmmm-gaussian --enable-mpi   then make   make install are it right? --- 11年11月10日，周四, Micha Ben Achim Kunze 写道：

[gmx-users] orca and Segmentation fault

dear sir :  I installed gromacs-orca for qm/mm ./configure --without-qmmm-orca --with--qmmm-gaussian --enable-mpi make make install MPI is lam-mpi   when run mdrun , the error " Back Off! I just backed up md.log to ./#md.log.12# Getting Loaded... Reading file pyp.tpr, VERSION 4.5.1 (single pre

Re: [gmx-users] orca and Segmentation fault

as reported here)." --- 11年11月14日，周一, Christoph Riplinger 写道： 发件人: Christoph Riplinger 主题: Re: [gmx-users] orca and Segmentation fault 收件人: "Discussion list for GROMACS users" 日期: 2011年11月14日,周一,下午6:51 Dear xi zhao, In your case GMX is applying threading and thus not only a s

[gmx-users] how to use atom2cg.awk

Dear Sirs:   I wang to know simulate coarse-graied system using gromacs, but I don not know how to use atom2cg.awk to convert CG model! Thank you very much! ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/__

Re: [gmx-users] how to use atom2cg.awk

Dear sir : how to motify the $5 in details? Thank you! --- 09年5月8日，周五, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] how to use atom2cg.awk 收件人: "Discussion list for GROMACS users" 日期: 2009年5月8日,周五,下午6:46 xi zhao wrote: > > > Dear Sirs: >   I

Re: [gmx-users] how to use atom2cg.awk

, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] how to use atom2cg.awk 收件人: "Gromacs Users' List" 日期: 2009年5月11日,周一,上午8:22 xi zhao wrote: > Dear sir : > how to motify the $5 in details? > Thank you! > Use a text editor (vi, emacs, gedit, etc), l

Re: [gmx-users] how to use atom2cg.awk

List" 日期: 2009年5月11日,周一,下午6:49 xi zhao wrote: > Dear Sir: > In fact, I have modified the script as you said, but the CG strucrute > produced is not different  in secondary strucure with native PDB structure: > CG structure became a line strucrue! Please help me! Or give me a

[gmx-users] how to perform Combined essential dynamics analysis and procedure!

Dear sir : Can you give me some information on Combined essential dynamics analysis and its procedure? Thank you! ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/___ gmx-users m

[gmx-users] how to plot free enenrgy landscape and exact corresponding conformation

Dear Users of Groamcs: ON the abasis of ED analysis, how to plot free energy landscape and exact corresponding conformation? Thank you very much! ___ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/-- gmx-users mailing list

[gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

Dear users for gromacs: We know that observing the sampled conformations in the subspace spanned by the eigenvectors is a so-called two-dimensional projection(2D projection), in 2-D projection, each point represents a snapshot from the simulation, and the distribution shows the sampled region along

Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

and extract the conformation from the trajectory. Cheers, Tsjerk 2009/12/20 xi zhao Dear users for gromacs: We know that observing the sampled conformations in the subspace spanned by the eigenvectors is a so-called two-dimensional projection(2D projection), in 2-D projection, each point repres

Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

Wassenaar 写道： 发件人: Tsjerk Wassenaar 主题: Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection 收件人: "Discussion list for GROMACS users" 日期: 2009年12月22日,周二,下午7:43 Ni hao Xi Zhao, Please note again that you're working with projection

Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

日期: 2009年12月23日,周三,下午7:26 Xi Zhao, I have no script either. It's not my homework, and I'm not on your payroll. If I need a script like that and write it, I'll be happy to share it with you. But that's not going to be soon. At present, I don't even have a data set to us

[gmx-users] how to analysis crystal structure and 2D projections by PCA?

Dear users: I want to analyse a crystal structure by PCA, and want to show its 2D projection, but I meet errors" segment fault" my procedure: g_covar_d -f crystal strucutre.pdb -s crystal strucutre.pdb  -o eig.xvg -v eig.trr g_anaeig_d -f  crystal strucutre.pdb -eig eig.xvg -v eig.trr -2d 2d.

[gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations

Dear gromacs users: How to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations; for example, software or script using, how to reconstruct PMF in detail? thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.g

[gmx-users] how to analye a single structure (NMR or X-ray) by PCA?

Dear sir : I want to analye a collective motions of a single structure by PCA , for example, how to choose reference structure using g_covar; how to show its position in 2D-projection (conformational space)? thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://l

Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations

through time series analysis of SMD or pulling simulations 收件人: "Discussion list for GROMACS users" 日期: 2010年3月24日,周三,下午9:58 xi zhao wrote: > Dear gromacs users: > > How to reconstruct potentials of mean force through time series analysis of > SMD or pulling simulations; fo

Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations

simulations 收件人: "Gromacs Users' List" 日期: 2010年3月24日,周三,下午10:10 xi zhao wrote: > dear Mr Justin A. Lemkul : > I have read your _tutorial ,it is suitable for umbrella sampling method, it > is not for SMD, wham or g_wham can not be used!_ > _Thnak you!_ > If you w

Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations

题: Re: [gmx-users] how to reconstruct potentials of mean force through time series analysis of SMD or pulling simulations 收件人: "Gromacs Users' List" 日期: 2010年3月24日,周三,下午10:10 xi zhao wrote: > dear Mr Justin A. Lemkul : > I have read your _tutorial ,it is suitable for umb

[gmx-users] coarse-grained model of POPC in Martini coarse-grained force field?

I'd like to run simulations with coarse grained model lipid bilayer.  I can not  find the force field for coarse grain POPC lipid or equilibrated bilayer coordinates in Martini website. Please help me! thank you! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

[gmx-users] Martini Cg-model can not be downloaded!

well.. it seems that there is a problem in the page for downloading files from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html, the cg model parameters can not be downloaded! Thank you for help! ___ 好玩贺卡等你发，邮箱贺卡全新上线！ h

[gmx-users] demux.pl

Dear all Gromacs users: I want to obtain demux.pl for analysis REMD, but I do not know how to get it, please help me! Thank you very much! - 雅虎邮箱传递新年祝福，个性贺卡送亲朋！ ___ gmx-users mailing listgmx-users@groma

回复： Re: [gmx-users] demux.pl

Sorry, but in source of v3.3.2 and 3.3.1 of the website , there is not demux.pl script, please help me! Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote: > Dear all Gromacs users: > I want to obtain demux.pl for analysis REMD, but I do not know how to > get it, please help

[gmx-users] about using amb2gmx.pl

Dear all users: I want to simulate a system ( protein + chromophore). I have had chromophore.gro and its top file using amb2gmx.pl,but I find I can not use them to translate PDB( protein + chromophore) file into gro and top files properly. So I need your advice about further procedure! Than

回复： Re: [gmx-users] about using amb2g mx.pl

Dear sir : Can you tell me a detail of procedure, I have only chromophore molecular top,but I need entire top and gro for pdb + chromophore! Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote: > Dear all users: > I want to simulate a system ( protein + chromophore). I

回复： Re: 回复： Re: [gmx-use rs] about using amb2gmx.pl

gt; 写道： xi zhao wrote: > Dear sir : > Can you tell me a detail of procedure, I have only chromophore molecular > top,but I need entire top and gro for pdb + chromophore! Your use of terminology is unclear - and you can't afford this sort of lack of clarity in science. pdb, gro and

回复： Re: 回复： Re: 回 复： Re: [gmx-users] about using amb2gmx.pl

Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding gro top files, but I can only produce chromophore gro and top file using amb2gmx.pl .Are you clear ? Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote: > Dear sir : > In fact, I have a complex structure(wh

回复： Re: 回复： Re: 回 复： Re: 回复： Re: [gmx-users] ab out using amb2gmx.pl

website. I do not know how to produce gro and top of entire system. Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote: > Easily, I have a pdb complex(pdb: 1O5P), I want to produce corresponding > gro top files, but I can only produce chromophore gro and top file using > amb2gmx.pl

回复： Re: 回复： Re: 回 复： Re: 回复： Re: 回复 � Re: [gmx-users] about using amb2gmx.pl

't really matter) you already have 2. What topologies you have, and how you generated them 3. Specific errors you are having (from pdb2gmx, etc), not simply "I cannot get top and gro for the whole complex." It leaves us wondering what you have or haven't tried doing. -Justin Quoti

回复： Re: 回复： Re: 回 复： Re: 回复： Re: 回复 � Re: [gmx-users] about using amb2gmx.pl

other gromacs tools. There may be other ways as well. Anyway, where you are at present is apparently step (3). Hope that helps. David 2008/2/17 Mark Abraham : > xi zhao wrote: > > Dear sir: > > Is my english weak? > > Not particularly, but it isn't helping you de

[gmx-users] how to remd analysi?

Dear all users: I performed remd using GROMACS 3.3.1,but I find that I do not know how to analyze the result further,though I have demux.pl script and produced replica_index.xvg and replica_temp.xvg files, the contents of two files are the same! I use trjcat_d to produce a continuous trajector

回复： Re: [gmx-users] how to remd ana lysi?

trajectories! Are you clear? Thank you for your help! Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote: > Dear all users: > I performed remd using GROMACS 3.3.1,but I find that I do not know how > to analyze the result further, "Analyze" really doesn't te

[gmx-users] 2D projection and corresponding conformation

Dear user: We know that observing the sampled conformations in the subspace spanned by the eigenvectors is a so-called two-dimensional projection(2D projection), in 2-D projection, each point represents a snapshot from the simulation, and the distribution shows the sampled region along the fir

回复： Re: [gmx-users] 2D projection and corresponding conformation

Dear sir : I also know these,but can you give some detail procedure for obtaining the corresponding conformations? Thank you in advance! Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote: > Dear user: > We know that observing the sampled conformations in the subspace spann

回复： Re: 回复： Re: [gmx-use rs] 2D projection and corresponding conformation

you give me some advise! ? Thank you very much! Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote: > Dear sir : > I also know these,but can you give some detail procedure for obtaining > the corresponding conformations? Thank you in advance! No, because you've told

[gmx-users] analysizing the sam.edo script?

Dear users: I want to analyze the EDS (essential dynamics sampling ) results (sam.edo file),though the website and manual both show that "parse_edo "can do it, I do not know how to get it,because I can not find it in the website. Please help me! -

[gmx-users] how to fix a position in the single eigenvector in essential dynamics sampling?

Dear users: I want to know: in EDS (essential dynamics sampling), how to fix the eigenvector ,while the other degrees of freedom wiil be equilibrated. how to set up? using the :linfix" in make_edi ? Please help me! Thank you very much! - 雅虎邮箱，您的终

[gmx-users] how to fix the COM of group in the pull.

Dear users: I want to know how to fix the com of the group in the pull or afm simulation,Please give some ideas. - 雅虎邮箱，您的终生邮箱！___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailm

[gmx-users] how to fix the center of mass of the protein in the pull simulation

Dear users: how to fix the center of mass of the protein in the pull simulation? I want to know to know! Please help me! - 雅虎邮箱，您的终生邮箱！___ gmx-users mailing listgmx-users@gromacs.org http://www.groma

[gmx-users] AFM and g_wham

Dear users: When I finished a AFM simulation and wanted to analyze the pdo file ,but g_wham can not run and report errors ,such as :"This does not appear to be a valid pdo file" or "You need to specify a series of pdo files as input", and mailing lists can not give me correct anwser. Please he

[gmx-users] pull.pdo and AFM force

All users: I want to calculate the AFM force in afm pulling, is there a script to obtain forces from afm pulling! In fact, g_wham can not run, it is very depressed. Please help me! Thank you in advance! - 雅虎邮箱，您的终生邮箱！

[gmx-users] InflateGRO and pentamer protein simulation

Dear sir : I want to a pentamer membrane protein, when I used InflateGRO.pl with DOUGHNUT Mode, the results were wrong, please help me! show " [u...@localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4 POPC 14 kk_inflated.gro 5 area.dat doughnut protein_subunits Doughnut mode activated.

Re: [gmx-users] InflateGRO and pentamer protein simulation

ein simulation 收件人: "Discussion list for GROMACS users" 日期: 2010年4月9日,周五,上午2:14 xi zhao wrote: > > > Dear sir : > I want to a pentamer membrane protein, when I used InflateGRO.pl with > /DOUGHNUT Mode, the results were wrong, please help me! / If you want any useful hel

Re: [gmx-users] InflateGRO and pentamer protein simulation

Dear sir: Thank you for your help! --- 10年4月11日，周日, shaya...@post.tau.ac.il 写道： 发件人: shaya...@post.tau.ac.il 主题: Re: [gmx-users] InflateGRO and pentamer protein simulation 收件人: jalem...@vt.edu, "Discussion list for GROMACS users" 日期: 2010年4月11日,周日,下午10:01 Dear Xi Zhao, For

[gmx-users] construct CG membrane protein and CG membrane and inflategro.pl

Dear Gromacs users: I use inflateGRO.pl to insert CG protein in to CG POPC membrane, but when carryied EM with Strong POStion REStraint, the protien and membrane were apart. Please help me! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gm

Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl

protein and membranr separate , --- 10年4月12日，周一, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl 收件人: "Discussion list for GROMACS users" 日期: 2010年4月12日,周一,下午8:42 xi zhao wrote: > > >

Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl

12日,周一,下午8:42 xi zhao wrote: > > > Dear Gromacs users: > I use inflateGRO.pl to insert CG protein in to CG POPC membrane, but when > carryied EM with Strong POStion REStraint, the protien and membrane were > apart. Please help me! What does "apart" mean?  If you

Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl

Users' List" 日期: 2010年4月12日,周一,下午9:07 xi zhao wrote: > > my procesure: > 1. cat cgprotein cgmembrane>system.gro (using Martini force field) Were these structures initially centered within the same coordinate system?  By your description, it sounds like these two compo

[gmx-users] how to show structure results in Martini coarse-grained simulation?

Dear user: how to show struture or conformation in Martini coarse-grained simulation, using VMD or other? Please give me some suggestion! thank you! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

op2psf.pl "Cannot open atoms for reading: No such file or directory" please help me! --- 10年5月3日，周一, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: "Discussion list for GROMACS users"

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

in fact, how to deal with format problem in coarse-grained ? thank you! --- 10年5月6日，周四, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: "Gromacs Users' List" 日期: 2010年5月6日,周四,上午9:40

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

produce input file , in coarse grained , no standard protein top file --- 10年5月6日，周四, Justin A. Lemkul 写道： 发件人: Justin A. Lemkul 主题: Re: [gmx-users] how to show structure results in Martini coarse-grained simulation? 收件人: "Gromacs Users' List" 日期: 2010年5月6日,周四,上午10:37

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

omacs Users' List" 日期: 2010年5月7日,周五,下午7:10 xi zhao wrote: > > Yes， I load my coarse-grained PDB ,then load ps as data, but the stucture > still was full of points . > Is a proper "!NBOND" section generated in your .psf file?  If the script finishes without an

Re: [gmx-users] how to show structure results in Martini coarse-grained simulation?

romacs.org/Developer_Zone/Programming_Guide/VMD -Justin xi zhao wrote: > > thank you for your help! > > 4 > <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844> > > --- *10年5月7日，周五, Justin A. Lemkul //* 写道：

[gmx-users] phosphated residue???

Dear all There is a phosphate ser in my protein, so when pdb2gmx, the fatal error is "atom p is not found" How to deal with this problem? how to add the topology file of phosphate ion to residue database? Thank you! - 雅虎免费邮箱3.5G容量，20M附件！_

[gmx-users] entropy calaculted script??

Dear Gro-usr friends: I want to calculat the entropy during the md,but lack calculting script for the entropy. Who can provide it for me? Thank you very much! - @yahoo.cn 新域名、无限量，快来抢注！___ gmx-users mailing lis

[gmx-users] g_energy has no bond entry when MD analysis

Dear friends: when my MD was finished and I want to analyse the bond energy of the protein ,but g_energy did not show bond entry: the first entry is angle? When energy miniumzation finished,g_energy did show G96 bond. why? Please help me! Thank you! -

回复： Re: [gmx-users] g_energy has no bond entry when MD analysis

Yes, I use bond constraints! Mark Abraham <[EMAIL PROTECTED]> 写道： > Dear friends: > when my MD was finished and I want to analyse the bond energy of the > protein ,but g_energy did not show bond entry: the first entry is angle? > When energy miniumzation finished,g_energy did show G96 bond. why?

回复： Re: [gmx-users] Is 2D projection

Dear sir : Can I understand" 2D projection = Component (PC) Probability Distributions P(v1,v2)"? If this is a true, and how to define the Pmax in detail? Thank you in advance! Nguyen Hoang Phuong <[EMAIL PROTECTED]> 写道： > Dear gmx users,>> Does the 2D projection plot has something to do with conv

回复： Re: 回复： Re: [gmx-use rs] Is 2D projection in g_anaeig

n der Spoel <[EMAIL PROTECTED]> 写道： xi zhao wrote:> Dear sir : Can I understand" 2D projection = Component (PC) Probability > Distributions P(v1,v2)"? If this is a true, and how to define the Pmax > in detail?> Thank you in advance! you can specify the vectors you wa

[gmx-users] Pobability of conformational distributions!

Dear sirs: How to calculate the probability of conformational distributions in gromacs by PCA method? I often meet it, but I do not know how to define it! The free energy = -KBTln(probability of conformational distribution). Thank you for your reply! Mp3疯狂搜-新歌热歌高速下

回复： Re: [gmx-users] Pobability of con formational distributions!

Dear sir: I can not konw how to use g_sham  combining with PCA? can you give me a example? Thank you very much! David van der Spoel <[EMAIL PROTECTED]> 写道： xi zhao wrote:> Dear sirs:> How to calculate the probability of conformational distributions in > gromacs by PCA method? I oft

[gmx-users] r.m.s.i.p

Dear Gromacs users: I am a new gromacs user, I want ro calculate r.m.s.i.p for exploring similar in motions of two different proteins, I need a script or tools to calculate it. I need your help! Thank you in advance! Best regard! __

回复： Re: [gmx-users] r.m.s.i.p

., Ceruso, M. A., Paci, M., Di Nola, A. & Berendsen, H. J. A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292.Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote:> Dear Gromacs users:> I am a new gromacs user, I w

回复： Re: [gmx-users] r.m.s.i.p

., Ceruso, M. A., Paci, M., Di Nola, A. & Berendsen, H. J. A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells. Proteins. 1999. 35, 283-292.Mark Abraham <[EMAIL PROTECTED]> 写道： xi zhao wrote:> Dear Gromacs users:> I am a new gromacs user, I w

回复： RE: [gmx-users] r.m.s.i.p

how to use it in detail?Thanks!"Fan, Fenghui " <[EMAIL PROTECTED]> 写道： Try RMSD fit function.-Original Message-From: [EMAIL PROTECTED] on behalf of xi zhaoSent: Mon 9/18/2006 2:12 AMTo: gmx-users@gromacs.orgSubject: [gmx-users] r.m.s.i.pDear Gromacs users:I am a new gromacs user, I want ro

回复： Re: 回复： Re: [gmx-use rs] r.m.s.i.p

Dear Tsjerk : Thank you very much!Tsjerk Wassenaar <[EMAIL PROTECTED]> 写道： Hi Xi Zhao,Please find attached a .csh script you can use to calculate the rmsip.The script is of the hand of Isabella Daidone, now in Heidelberg.Note that for a set of 'equal' simulations there is a spr

回复： Re: 回复： Re: [gmx-use rs] r.m.s.i.p

arajOn Mon, 18 Sep 2006 16:15:43 +0800 (CST), "xi zhao"<[EMAIL PROTECTED]>said:> Based on the essential dynamics analysis, the similar of the internal> fluctuations in may simulation systems was evaluated by comparing> principal subspace first 10 eigenvectors) of each structura

回复： Re: [gmx-users] PMF calculation

Dear Mr Mark Abraham: Can you tell us the details of performing PMF procedures? Thank you very much! Best wish for you! Mark Abraham <[EMAIL PROTECTED]> 写道： > Dear all, > I am working on a tripeptide and would like to calculate Potential > Mean Force for the tripeptide. Suggestions to cal

回复： [gmx-users] about PMF calculation

try mdrun_d and g_wham: Can you tell me how to produce pdo file? thank you very much! 黄永棋 <[EMAIL PROTECTED]> 写道： Hi gmx-users I am a gromacs beginner, I want to do the PMF calculation ,I have done as the manual said ,I added the ppa, ndx files and got a pdo file . But I don't know