[gmx-users] qmmm temp definition

Hi gmxers, I am working on qmmm treatment of a heat shock protein. Heat-sensitive part is treated quantum mechanically, while the other parts classically. I am hence wondering if it is available and applicable in gromacs that this qm part can be heated and cooled for temperature variation purpose

[gmx-users] qmmm linking atom

Hi gmxers, I am just wondering how to give a linking atom's coordinates in a qmmm calculation generally.Would it be normal to take an arithmetic average of two neighboring qmmm-layer-bonding atoms' coordinates? Thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

[gmx-users] QMMM+NMA

Hi Gmxers, I am wondering if NMA has been introduced into QMMM part of gromacs. I am trying to get vibrational frequencies of proteins by normal mode analysis (NMA) in the framework of QMMM. Thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listin

[gmx-users] protein in solution

Hi Gmxers, I plan to simulate a protein in an 1M glycerol solution. How can I control the concentration and "insert" the protein into my solution. Thanks, Yao  -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] co-solvent simulation

I am simulating a protein in glycerol solution in amber03 ff and followed "http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents";. Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp and aminoacids.rtp. For test purpose, I then made a itp for it and sol

[gmx-users] co-solvent simulation

I am simulating a protein in glycerol solution in amber03 ff and followed "http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents";. Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp and aminoacids.rtp. For test purpose, I then made a itp for it and

Re: [gmx-users] co-solvent simulation

anks, Yao From: Mark Abraham To: Discussion list for GROMACS users Sent: Saturday, February 11, 2012 9:39 PM Subject: Re: [gmx-users] co-solvent simulation On 12/02/2012 4:16 PM, Yao Yao wrote: I am simulating a protein in glycerol solution in amber03 ff and follo

[gmx-users] co-solvent simulation

he same problem before. Thanks, Yao - Forwarded Message ----- From: Yao Yao To: Discussion list for GROMACS users Sent: Saturday, February 11, 2012 10:47 PM Subject: Re: [gmx-users] co-solvent simulation Hi Mark, Thanks for your reply. I have not figured out what the problem. BUt I am

Re: [gmx-users] co-solvent simulation

Please disregard my previous email. I made a minor mistake when I built the .top file. Thanks, Yao From: Yao Yao To: "gmx-users@gromacs.org" Sent: Saturday, February 11, 2012 11:06 PM Subject: [gmx-users] co-solvent simulation Actually eve

[gmx-users] water channel

Hi Gmxers, Happy Valentine's Day! Sorry, I am still simulating a protein that has water channel. I was just wondering if there is a way to calculate the water density in the channel throughout my trajectory. I was lucky enough to run a NPT simulation. So I guess I can use g_energy to directly

[gmx-users] Water Shell Density

Hi Gmxers, Is there a way to calculate the density of water in a protein hydration layer, like from 5 A to 10 A (radius) from the protein surface? Thanks, Yao-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

[gmx-users] Water Shell Density

Hi Gmxers, Is there a way to calculate the density of water in a protein hydration layer, like from 5 A to 10 A (radius) from the protein surface? Thanks, Yao -- gmx-users mailing list    gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] hessian conversion

Hi Gmxers, has anyone ever converted the GROMACS hessian (in ps^(-2)) to CHARMM hessian (in KCal/mol), even considering the individual unit, GROMACS hessian numbers are far bigger than those in CHARMM? thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/m

Fw: [gmx-users] hessian conversion

Hi Gmxers, has anyone ever converted the GROMACS hessian (in ps^(-2)) to CHARMM hessian (in KCal/mol), even considering the individual unit, GROMACS hessian numbers are far bigger than those in CHARMM? thanks, Yao -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.grom

[gmx-users] Gmx Hessian

hi Gmxers, is the Hessian matrix unit in gmx is ps^(-2), or J *mol^(-1) nm^(-2)? thanks, Yao -- 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 postin

[gmx-users] Hessian Unit

hi Gmxers, is the Hessian matrix unit in gmx is ps^(-2), or J *mol^(-1) nm^(-2)? thanks, Yao -- -- 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 be

[gmx-users] NMA Fatal Error

Hi Gmxers, I am doing a protein NMA with the mdp file like, === define  = -DEFLEXIBLE constraints = none integrator  = nm ; emtol   = 0.1 emstep  = 0.1 nsteps  = 4000  ; Maximum number of (minimization) steps to

[gmx-users] NMA proctocol

guarantee the convergence, or I have to await luck to come. Because I am pretty sure if I continue with NMA, I will get translational and rotational modes in final eigenfrequencies. thanks, Yao   On 11/16/12 3:43 PM, Yao Yao wrote: > Hi Gmxers, > > I am doing a protein NMA with the mdp

[gmx-users] Mopac/Gmx QMMM

I am trying to compile mopac with gmx for qmmm calculation purpose and found the link  http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMMis really helpful. However I can only download the on of the two required fortran files, gmxmop.f,but not the other, dcart.f. And since

[gmx-users] QMMM Semi-empirical Error

e? Thanks, Yao Yao-- 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 interfac

[gmx-users] Fw: QMMM Semi-empirical Error

is before? Thanks, Yao Yao-- 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 in

[gmx-users] g_hbond simple question

Hi Guys, I am using g_hbond to analyze hbond between two groups. The manual says "All hydrogen bonds between the two groups are analyzed." Does that mean even those hbonds do not hbond to neither of the two groups are still under consideration? Thanks, Yao -- gmx-users mailing listgmx-use

[gmx-users] OPLS-AA Unknown Atomtype

Hi all, I am constructing a new molecule in OPLS force field. Though I modified ffbonded.itp, ffnonbonded.itp, atomtypes.atp aminoacids.rtp, it still gives error "Unknown Molecule_Atomtype". I have opened all the files in the OPLS force field but really do not see any other files I could modify

Re: [gmx-users] OPLS-AA Unknown Atomtype

y declared those values in the ffoplsaabon.itp.  Is there any other file I also need to mention those values? Thanks, Yao From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Tuesday, August 23, 2011 2:07 PM Subject: Re: [gmx-users] OPLS-AA Unk

Re: [gmx-users] OPLS-AA Unknown Atomtype

to modify. Thanks, yao From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Monday, August 29, 2011 3:41 AM Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype Yao Yao wrote: > Hi Justin, > > Thanks for your last reply. Now it seems

[gmx-users] pdb2gmx response time

Hi All, when I pdb2gmx on a very small (~20 atoms) peptide, it seemingly got stuck in the middle, showing Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.rtp Opening library file /share/apps/gromacs407/share/gromacs/top/aminoacids.dat Opening library

[gmx-users] gbsa.itp problem

Hi All, when I grompp for energy minimization, I met the error like, -- Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs40

Re: [gmx-users] gbsa.itp problem

is there any other file I need to change? thanks, yao From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Tuesday, September 6, 2011 3:21 PM Subject: Re: [gmx-users] gbsa.itp problem Yao Yao wrote: > Hi Justin, > > Thanks for your

[gmx-users] QM/MM/MD Semi-empirical Error

orted" -- I googled it, but there seems no archived info online. Has anyone met this before? Thanks, Yao Yao -- gmx-users mailing list    gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archiv

[gmx-users] QM/MM/MD Semi-empirical Error

, yao - Forwarded Message - From: Yao Yao To: "gmx-users@gromacs.org" Sent: Tuesday, September 13, 2011 12:14 AM Subject: [gmx-users] QM/MM/MD Semi-empirical Error Hi Guys, I met a problem when I ran QM/MM/MD using semi-empirical method in gmx

[gmx-users] where are Density and Volume?

Hi, I wanna get Density and Volume of my system after simulation. I found in tutorials by Justin and kerrigan?, that g_energy -f *.edr -o should work, but I do not find in my version 4.5.1 and 4.5.4. That is kind of weird. Thanks, Yao-- gmx-users mailing listgmx-users@gromacs.org http://li

Re: [gmx-users] where are Density and Volume?

Hi Justin, thanks, that is just initial value, no fluctuation over time. yao   From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Thursday, October 13, 2011 10:24 AM Subject: Re: [gmx-users] where are Density and Volume? Yao Yao wrote

Re: [gmx-users] where are Density and Volume?

From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Thursday, October 13, 2011 10:42 AM Subject: Re: [gmx-users] where are Density and Volume? Yao Yao wrote: > Hi Justin, > > thanks, > > that is just initial value, no fluctu

Re: [gmx-users] where are Density and Volume?

using it for the same time length simulation, do you happen to know the reason? Thanks, yao From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Thursday, October 13, 2011 11:28 AM Subject: Re: [gmx-users] where are Density and Volume? Yao Yao

[gmx-users] g_hbond frames

Hi Gmxers, I ran g_hbond between my protein and water for a 3ns trajectory with 2 fs integration step but found the error, "Cannot calculate autocorrelation of life times with less than two frames", I am quite sure my system is just a regular protein in a cubic water box. And the size of traj

[gmx-users] solvents in gmx

Hi Gmxers, Is there a way I can check all the kinds of solvents in gromacs? Apart from water, ethanol, ..., are there any Glycerol, Treholose, Thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at h

[gmx-users] g_hbond -hbn

Hi Gmxers, I used g_hbond -n protein.ndx -hbn output.xvg to get the index of all the atoms forming H-bond with the protein, but since H-Bonds should be dynamic as time evolves, I should see changing number of HBonds in the output.xvg which I have not seen yet. Kinda confused. Thanks, Yao 

[gmx-users] protein hydration shell water

Hi Gmxers, Anyone knows any command or flag that can extract the water within some distance from the surface of a protein? thanks, Yao Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] g_select dynamic indices

Hi Gmxers, I used g_dist to find all water molecules within 5 Angstrom of a protein in a trajectory with a little surprise that gromacs directly prints out those water on my screen rather than in an output file. Since in each frame, those water molecules are not the same, I realize I need to ma

[gmx-users] g_select dynamic indices

to "Select a group", I am wondering if I can make this "choice" in a script rather than when I see the prompt. thanks, Yao From: Justin A. Lemkul To: Yao Yao ; Discussion list for GROMACS users Sent: Wednesday, November 30, 2011 1:57

[gmx-users] g_hbond segmentation fault

-- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915Segmentation fault __ Hi guys, I got the msg like above when

[gmx-users] Fw: g_hbond segmentation fault

-- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915Segmentation fault __ Hi guys, I got the msg like above w

Re: [gmx-users] Fw: g_hbond segmentation fault

iscussion list for GROMACS users" > Date: Tuesday, September 28, 2010, 6:22 PM > > > > > > >

[gmx-users] g_hbond segmentation fault

Hi Gmxers, I used the command line,  g_hbond -f tst.trr -s tst.tpr -ac test -e 500 -dt 1 and I got the message like, -- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and

[gmx-users] g_hbond segmentation fault

9, 2010, 6:11 AM On 2010-09-29 08.02, Yao Yao wrote: > Hi Gmxers, > > I used the command line, > > g_hbond -f tst.trr -s tst.tpr -ac test -e 500 -dt 1 > > and I got the message like, > try without the -dt 1 > -- > Found 1048 different h

[gmx-users] g_hbond segmentation fault

>    > >      >    >    >     Hi, > >      > >     Could you file a bugzilla and attach the trr and tpr > files please? >     If you do I'll try to sort it out today or at least > this we

[gmx-users] charmm tip5p in Gmx 4.5.2

Dear Gmxers, Does anyone have an idea about what time the Gmx 4.5.2 will be released?And in 4.5.2, would the modified tip5p.itp in charmm27 force field be the same as that in current git version? Thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mai

[gmx-users] charmm tip5p in Gmx 4.5.2

--- Begin Message --- Dear Gmxers, Does anyone have an idea about what time the Gmx 4.5.2 will be released?And in 4.5.2, would the modified tip5p.itp in charmm27 force field be the same as that in current git version? Thanks, Yao --- End Message --- -- gmx-users mailing list

[gmx-users] charmm tip5p in Gmx 4.5.X

Hi Berk, Thanks for your reply. Actually I followed the fws-peptide simulation in Dr. JE Kerrigan's tutorial, but in charmm27 force field with tip5p water. Before several warnings in the simulation step, I found that even in energy minimization step the protein cannot be settled. I sent my m

[gmx-users] Targeted Energy Minimization

Hi Gmxers, Is that possible that in mdp file, only a specifically-targeted part inside/of the protein is energy minimized (EM)? Like, just wanna EM the ligand or one out of the two proteins in protein-docking. Thanks in advance, Yao -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] NMA

HI Gmxers, Anyone came across a step-by-step tutorial for normal mode analysis, not a theoretical background introduction but a practical hands-on demonstration in gromacs? I dunno what steps to follow. Thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.grom

[gmx-users] Eigenvectors

Hi Gmxers, I am just wondering if the eigenvectors in gromacs are normalized or not, and how to check that after the normal mode analysis/ thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at h

[gmx-users] Eigenvectors

Hi Gmxers, I am just wondering if the eigenvectors in gromacs are normalized or not, and how to check that after the normal mode analysis/ thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at h

[gmx-users] Eigenvectors

> Hi Gmxers, > > I am just wondering if the eigenvectors in gromacs are > normalized or not. > thanks, > > Yao -- 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/Maili

[gmx-users] tip5p.itp in Charmm

Hi, I am running charmmm force field (ff) in gmx 4.5 version and just trying on tip5p water model in it. Unfortunately I only find tip5p.gro is in the ff, not tip5p.itp file. Can anyone help me with hints on constructing it? Many thanks, Yao -- gmx-users mailing listgmx-users

[gmx-users] OWT5 not found in Charmmff

I am running tip5p in charmm force field in gmx. In energy minimization step, it gives an error msg as below. I just simply added it in atomtypes.atp in charmm27.ff, but still it doesn't work. Does anyone know how to solve it? Many thanks, Yao ---

[gmx-users] Fw: NO GSL! Can't find and take away ballistic term in ACF without GSL

--- On Tue, 9/14/10, Yao Yao wrote: Dear Gmxers, > I met this msg when running g_hbond > in 4.5-beta version. > Then it gives "Segmentation Fault" without any time frame > reading. > Does anyone know what it means? > > thanks, Yao >       > -

[gmx-users] NO GSL! Can't find and take away ballistic term in ACF without GSL

I met this msg when running g_hbond in 4.5-beta version. Then it gives "Segmentation Fault" without any time frame reading. Does anyone know what it means? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] 4.5 Installation failure

Hi Gmxers, I was trying to install gmx 4.5 after installing the most recent fftw package in the same directory. Then I extracted gmx and ran ./configure and make, but it showed   "make: *** No targets specified and no makefile found.  Stop." Anyone know what I did wrong? Thanks, Yao