Re: [gmx-users] RMSD

I think what you really need is not Gromacs. For example, you can use UCSF Chimera to get alignment and RMSD between two PDBs. dawei On Wed, Jan 23, 2013 at 10:38 AM, Shima Arasteh wrote: > > > Hi, > > Is it possible to get RMSD of 10 different pdb files by GROMACS? > g_rms may help? > > >

[gmx-users] ensemble distance restraints

Dear All I tried to run MD with ensemble based distance restrain. I set disre=Ensemble and use -multi command argument in mdrun, according to the manu. However, gromacs4.6 give me an error "Sorry, distance restraints with ensemble averaging over multiple molecules in one system are not functional

Re: [gmx-users] Question about 'mdrun -nosum'

I think the same way as you. They do bring in errors but this is acceptable in normal MD because we already have lots of approximations. BTW, -sum has been dropped from 4.5, in other words, Gromacs won't calculate global Energy every step by default now. dawei On Fri, Dec 14, 2012 at 9:46 AM, Th

Re: [gmx-users] particle decomposition with distance restraints

Dear Mark Here it is some information that may be useful. I checked all my -pd, with distance restraints MD runs. It seemed that crash usually happened when protons and the carbon they attached were in different processors. best, dawei On Thu, Dec 13, 2012 at 4:12 PM, Da-Wei Li wrote

Re: [gmx-users] particle decomposition with distance restraints

d to say much. > 3) Generally, turning off the restraints is not a proper solution (and > particularly not without adjusting the time step accordingly) - see > http://www.gromacs.org/Documentation/Terminology/Blowing_Up > 4) We're a long way from supposing there's a code bug :-) > &

Re: [gmx-users] Re: Can Gromacs functions be called by some other codes?

In your own code, you should have a system call function, which can be used to run any command in your system. Using C as example, you can write source code like this. /***/ system("g_rms -s xx.tpr -f xx.trr -o rmsd.xvg"); read in file rmsd.xvg t

Re: [gmx-users] Can Gromacs functions be called by some other codes?

>From your description, why not just write a script to run various Gromacs programs (MD, analysis, etc)? dawei On Tue, Jun 12, 2012 at 2:43 PM, Bao Kai wrote: > Hi, all, > > I am wondering if Gromacs functions can be called by some other codes. >  I know we get some library files and header file

Re: [gmx-users] RE:RE: gromacs installation

Usually /tmp is writable for any user. It looks like this is not a case in your system. Ask your system administrator. dawei On Tue, Oct 11, 2011 at 2:57 PM, Chunxia Gao wrote: > sorry, I wrote it wrong, actually I had added "./configure > --prefix=/home/yourname/..." in it, but it showed th

Re: [gmx-users] How to suppress the screen info & how to overwrite files?

It is possible that the terminal that used to run gromacs does not have GMX_MAXBACKUP set up. if you use some queue software, put "export GMX_MAXBACKUP=0" in the submitting script or even put it into your .bashrc file. On Fri, Aug 12, 2011 at 1:53 PM, Hiroshi Fujisaki wrote: > Dear Justin, > > T

Re: [gmx-users] mdrun crashes with 'One or more interactions were multiple assigned in the domain decompostion'

hello Just to share information. My parallel MD run also crash (very rarely) but I can always bypass the crash point using cpt files. dawei On Fri, Aug 12, 2011 at 10:02 AM, Sebastian Breuers wrote: > Hey, > > thank you both for the response. I at least could restart the system. And > it is run

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

Hello Please see my response below. On Thu, Aug 11, 2011 at 10:23 AM, Mark Abraham wrote: > On 11/08/2011 10:22 PM, Da-Wei Li wrote: > > Dear Mark and others > > I did more tests and thought that it might come from numerical error. The > reasons are > > 1. If I use .trr

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

/PBSA type calculation. The error is just too large. best, dawei On Thu, Aug 11, 2011 at 9:03 AM, Justin A. Lemkul wrote: > > > Da-Wei Li wrote: > >> Dear Justin >> >> An implicit water simulaiton with this short cutoff is problematic but I >> think it is fin

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

at I don't think this is the cause. best, dawei On Thu, Aug 11, 2011 at 8:47 AM, Justin A. Lemkul wrote: > > > Da-Wei Li wrote: > >> Dear Mark and others >> >> I did more tests and thought that it might come from numerical error. The >> reasons are >&

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

Dear Mark and others I did more tests and thought that it might come from numerical error. The reasons are 1. If I use .trr file instead of the low precision xtc file, things become better, ie, I get much less snapshots that has high energy. 2. I supplied -pforce in my mdrun -rerun and found tha

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

2011 at 11:32 AM, Mark Abraham wrote: > On 11/08/2011 1:18 AM, Da-Wei Li wrote: > > Dear Mark > > That is my thought too.To test this possibility, I created a mdp file > without PBC and use trjconv -pbc nojump to make whole protein. >From > visualization in UCSF Chimera, the

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

, 2011 at 11:12 AM, Mark Abraham wrote: > On 11/08/2011 12:29 AM, Da-Wei Li wrote: > >> Dear Gromacs users: >> >> I recently tried some MM/PBSA stuff using the rerun function of mdrun and >> GBSA model. All water molecules are stripped off the trajectory file. >

[gmx-users] strange vdw energy from rerun with GBSA model.

Dear Gromacs users: I recently tried some MM/PBSA stuff using the rerun function of mdrun and GBSA model. All water molecules are stripped off the trajectory file. However, when I examine the different energy term, it is disturbing that short range vdw energy of some snapshot are very high (> 100

Re: [gmx-users] oplsaa vs. charmm

re of the IDP in complex with its partner, carry out REMD > to unfold it, and then add an inhibitor to see where it binds. > > > You comments about the proposed protocol, force field and water model to > use, will be highly appreciated! > > thanks, > Thomas > > > > &g

Re: [gmx-users] oplsaa vs. charmm

I really don't think you can get adequate sampling for IDPs that have 40 residues, using full atomic MD. On Wed, Jun 8, 2011 at 3:25 PM, Michael Daily wrote: > Do you have some experimental data to compare to your IDP simulations, > like X-ray scattering or some such? I'd imagine that IDP simu

Re: [gmx-users] scaling non-bonded interactions

I remember that 1-4 won't be scaled in the free energy code, right? dawei On Wed, Jun 1, 2011 at 3:24 PM, Justin A. Lemkul wrote: > > > Kukol, Andreas wrote: > >> Hello, >> Is it possible to globally scale all non-bonded interactions by a factor ? >> I know there are energy exclusion groups, b

Re: [gmx-users] scaling non-bonded interactions

hello I do not know whether there is an option but you can achieve this easily by revising top file. dawei On Wed, Jun 1, 2011 at 4:59 AM, Kukol, Andreas wrote: > Hello, > > Is it possible to globally scale all non-bonded interactions by a factor ? > I know there are energy exclusion groups,

[gmx-users] difference of protein dynamics between NPT and NVE ensemble?

Hello, everyone, Does anyone have experience of doing NVE simulation? I wish to know, for a system with box size 6.1*6.1*6.1nm, whether the microcanonical ensemble for a NVE simulation will converge with the canonical ensemble from a NPT simulation? Thanks, -- gmx-users mailing listgmx-users

[gmx-users] Free energy calculation and position restraint

Dear all >From Table 5.6 of Gromacs 4.5.4 manu, position restrain constants can be interpolated in free energy calculations. However, I cannot find how to set up this. Can somebody help? thanks. dawei -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

Re: [gmx-users] free energy blank dgdl

hi It seems that your couple-moltype is missing, that is, no molecules will be turned off interaction. dawei On Thu, Feb 17, 2011 at 8:26 AM, Moeed wrote: > Hello Justin > > Thanks for your attention. Just to remind you: I am getting blank dgdl and > I found this in log file: > > > There are

Re: [gmx-users] Re: free energy calculation , grompp crash

hello Now it is almost clear what happened. When couple-intramol is no (default), all pairwise vdm and charge interaction becomes bonded interaction. All intra-molecular non-bonded interactions for moleculetype couple-moltype are replaced by exclusions and explicit pair interactions. In this m

Re: [gmx-users] Re: free energy calculation , grompp crash

-neutral -conc 0.001 -pname > NA -nname CL -g protein_ion.log -p protein.top > > Then I will grompp and mdrun. I seldom change these values. > > Thank you, > TJ Musard > > > > > On February 7, 2011 at 1:08 PM Da-Wei Li wrote: > > hi, all > I get another s

Re: [gmx-users] Re: free energy calculation , grompp crash

Minimum cell size due to bonded interactions: 4.960 nm so that domain decomposition will not work. What is a LJC pair? I did not see any problem with my system. Everything is fine if free_energy = no. thanks. dawei On Mon, Feb 7, 2011 at 1:38 PM, Da-Wei Li wrote: > hello > > My goal is

Re: [gmx-users] Re: free energy calculation , grompp crash

a MD(sd) > with FEP on after the PR? > > > > And are you doing hydration of a protein? > > > > Thank you, > > TJ Mustard > On February 7, 2011 at 10:23 AM "Justin A. Lemkul" > wrote: > > > > > > > Da-Wei Li wrote: > >

Re: [gmx-users] Re: free energy calculation , grompp crash

: > Dawei, > > > > I have no problems with proteins in the thousands of atoms. Can you post > your command line and mdp files? > > > > Thank you, > > TJ Mustard > > On February 7, 2011 at 9:31 AM Da-Wei Li wrote: > > Well. It actually isn't dead

[gmx-users] Re: free energy calculation , grompp crash

Well. It actually isn't dead but becomes very slow for large proteins. dawei On Mon, Feb 7, 2011 at 11:44 AM, Da-Wei Li wrote: > hi, > > I did more test and found that it depended on size of the protein. Grompp > will die when number of atoms of the protein is larger than

[gmx-users] Re: free energy calculation , grompp crash

hi, I did more test and found that it depended on size of the protein. Grompp will die when number of atoms of the protein is larger than about 200. Is it possible the source code limit the size of the protein that can be decoupled? thanks. dawei On Mon, Feb 7, 2011 at 10:34 AM, Da-Wei Li

[gmx-users] free energy calculation , grompp crash

Dear users I tried free energy calculation but grompp couldn't go through. It stops after *** Generated 2278 of the 2278 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2278 of the 2278 1-4 parameter combinations Excluding 3 bonded neighbours m

Re: [gmx-users] About parallel installation of GMX-4.5.1

I think you are right. 2010/9/11 wuxiao : > Dear GMXers, >   I have a quad-core computer at hand, on which I would like to install a > parallel implementation of GMX-4.5.1. The homepage > (http://www.gromacs.org/About_Gromacs/Release_Notes/Version_4.5) refers to > "running on a multi-core node now

Re: [gmx-users] Gromacs-4.5 (final) is out!

The download link seems wrong on Gromacs webpage. It links to beta4. dawei On Wed, Sep 1, 2010 at 4:10 PM, Rossen Apostolov wrote: > > It is finally here: *Gromacs-4.5* has been just > released. > All critical issues have been resolved to

Re: [gmx-users] New beta release: 4.5-beta3

According to our HPC manage, our MVAPICH2's version is 1.0.3. thanks for the information. dawei On Wed, Aug 11, 2010 at 2:52 PM, Roland Schulz wrote: > MVAPICH2 >=1.4.1 should be fine. Did you use a version <1.4.1? > On Wed, Aug 11, 2010 at 2:45 PM, Da-Wei Li wrote: >

Re: [gmx-users] New beta release: 4.5-beta3

Yes it is. Now everything is fine with openmpi instead of mvapich2. dawei On Wed, Aug 11, 2010 at 12:59 AM, Mark Abraham wrote: > > > - Original Message - > From: Da-Wei Li > Date: Wednesday, August 11, 2010 6:23 > Subject: Re: [gmx-users] New beta release: 4.5-beta

Re: [gmx-users] New beta release: 4.5-beta3

Hi,all Unfortunately, it still crash. Here it is the output of mdrun. Both Gromacs-4.0.7 and non-parallel 4.5b3 work fine on this system. I use mvapich2 and intel compiler. *** Getting Loaded... Reading file em.tpr, VERSION 4.5-beta3 (single precision) Loaded with Money

Re: [gmx-users] GROMACS-4.5-beta1 is out!

Hello I tried the Gromacs 4.5 beta. However, my MPI mdrun died. Here it is the output. The Gromacs-4.0.7 work fine for the same system. It is "protein in water" system. There are about 22000 atoms. *** Will use 9

Re: [gmx-users] Tabulated potentials and performance

I remember the manu states that it won't cost too much compared with standard potential function form. dawei On Mon, Jul 19, 2010 at 1:22 PM, ms wrote: > On 19/07/10 17:32, Da-Wei Li wrote: >> >> It will be very little from my experience. Remember that the dominate >&

Re: [gmx-users] Tabulated potentials and performance

It will be very little from my experience. Remember that the dominate part is the non-bonded force calculation. dawei On Mon, Jul 19, 2010 at 12:22 PM, ms wrote: > Hi, > > Do you know where can I find some information on how using tabulated > potential affects gmx performance, and how? I have to

Re: [gmx-users] Avoid generation of angles, pairs and dihedrals from pdb2gmx

You can just delete them in the generated top file. dawei On Fri, Jul 16, 2010 at 10:45 AM, C. Batistakis wrote: > Dear all > > According to the manual, pdb2gmx generates all the angles, pairs and > dihedrals automatically in a polymer chain. Because I need nothing of them > do you know any fas

Re: [gmx-users] Re: gromacs with CMAP

hi, all Finally figured out that it was because all numbers in the cmap.itp file must be separated by only one space,otherwise the program will read in a "zero". I would suggest this to be fixed in the release version. have a nice day. dawei On Tue, Jun 29, 2010 at 9:05 AM, Da-Wei

Re: [gmx-users] Re: gromacs with CMAP

else? > > /Per > > > 29 jun 2010 kl. 14.45 skrev Da-Wei Li: > >> HI, David, >> >> thanks for your advise. I remove the bond angle force and get same >> result. It is really strange. If I set +5 on all the 24*24 grid, I >> just get a inverted distributio

[gmx-users] Re: gromacs with CMAP

HI, David, thanks for your advise. I remove the bond angle force and get same result. It is really strange. If I set +5 on all the 24*24 grid, I just get a inverted distribution and if I set 0 on all grid, I will get a uniformed distribution. It is like that 27 regions are force to have zero cmap

[gmx-users] Re: gromacs with CMAP

> Hi, all > > I recently download the git version and test the CMAP. However, very > strange result I get. I want to use CMAP support in my own > coarse-grained force field. > > Basically, I construct a ALA-ALA-ALA system and turn off all energy > terms except bond length, bond angle and CMAP to do