[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

[gmx-users] NMA proctocol

to 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 file like

[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

[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

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

[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

[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

[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

[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

From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org 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

[gmx-users] co-solvent simulation

. Thanks, Yao - Forwarded Message - From: Yao Yao ya...@ymail.com To: Discussion list for GROMACS users gmx-users@gromacs.org 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

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 ya...@ymail.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Saturday, February 11, 2012 11:06 PM Subject: [gmx-users] co-solvent

[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] 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

[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 jalem...@vt.edu To: Yao Yao ya...@ymail.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent

[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_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] 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

[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

[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

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

are Density and Volume? Yao Yao wrote: Hi Justin, It is NVE. Is there a consistent way I can know my D and V? Then you've got the same case as NVT (for these values, anyway) - volume and density are fixed at whatever value they started at.  editconf should have printed this somewhere along

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

From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org 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

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

are Density and Volume? Yao Yao wrote: Hi, Justin Ok, I see the problem. Like your tutorial, I used cpt for NVT/NPT to mdrun/continue NVE production run. So though I did not set V or P constraint in NVE mdp, it still keeps them as constant, like my NVE did not work. Am I supposed to do

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

-- 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 archive at http

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

, yao - Forwarded Message - From: Yao Yao ya...@ymail.com To: gmx-users@gromacs.org 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

[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

Re: [gmx-users] gbsa.itp problem

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

[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

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

Unknown Atomtype Yao Yao wrote: Hi Justin, Thanks for your reply. Here is the exact error message, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology

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

to modify. Thanks, yao From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, August 29, 2011 3:41 AM Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype Yao Yao wrote: Hi Justin, Thanks for your

[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.

[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 list

[gmx-users] QMMM Semi-empirical Error

, 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 interface or send

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

? 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 interface or send

[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+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

[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

[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

[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

[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

[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

[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

[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

[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

[gmx-users] charmm tip5p in Gmx 4.5.2

---BeginMessage--- 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] g_hbond segmentation fault

, 2010, 7:55 AM                        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 week.            Erik            Yao Yao skrev 2010-09-29 08.22

[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

[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

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

segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, September 28, 2010, 6:22 PM Yao Yao skrev 2010-09-28 19.25

[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] 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

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

--- On Tue, 9/14/10, Yao Yao ya...@ymail.com 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 mailing listgmx-users

[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] 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] 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 list