Re: [gmx-users] Re: do_dssp

On 5/04/2012 4:16 PM, bharat gupta wrote: Yes , I am using the correct options for dssp. But still I am getting the same error. What does invoking /usr/local/bin/dsspcmbi say? Mark On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham > wrote: On 5/04/2012 10:25

Re: [gmx-users] Re: do_dssp

*This is the output : [root@BHARATPC ~]# /usr/local/bin/dssp bash: /usr/local/bin/dssp: Permission denied I have already set the pat for dssp in .bashrc using export command , I don't know why this error is there. Is it due to renaming dsspcmbi to dssp ?? * On Thu, Apr 5, 2012 at 4:08 PM, Mark

Re: [gmx-users] Re: do_dssp

On 5/04/2012 5:16 PM, bharat gupta wrote: /This is the output : [root@BHARATPC ~]# /usr/local/bin/dssp / Don't run as root except for installing software, unless you like rebuilding your computer from the ground up. /bash: /usr/local/bin/dssp: Permission denied / Possibly you didn't giv

Re: [gmx-users] Re: do_dssp

Ok now after downloading the latest version of dssp, and giving right permissions and after executing the /usr/local/bin/dssp command I am getting the following output :- [root@BHARATPC peptide2]# /usr/local/bin/dssp DSSP options: -h [ --help ] Display help message -i [ --input ] arg

[gmx-users] Another do_dssp problem

Dear Gromacs gurus, Forgive me for starting another topic on do_dssp. I encountered a somewhat different problem with the program. The environment and dssp permission setup are (supposedly) OK, but the dssp stuck at frame 0. do_dssp -f md.trr -s md.tpr -e 200 ... Selected 5: 'M

[gmx-users] how to change the timestamp of a xtc file

Hi, A quick question, how can I change the .xtc file which beginning at 0, end at 1 ns to beginning at 5ns and end at 6ns. Thanks for any suggestions, Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive a

[gmx-users] Monitoring of Salt bridges during simulation Run

Dear Gromacs Users! I'd like to monitor origin and destabilisation of salt-bridges during simulation time. In particular I want to define some charged residues within selection groups to monitor both of intra-protein as well as protein-protein interactions. In past I've used only g_hbond

Re: [gmx-users] Monitoring of Salt bridges during simulation Run

You can use g_saltbr option , http://manual.gromacs.org/online/g_saltbr.html On Thu, Apr 5, 2012 at 5:23 PM, James Starlight wrote: > Dear Gromacs Users! > > > I'd like to monitor origin and destabilisation of salt-bridges during > simulation time. In particular I want to define some charged resi

Re: [gmx-users] Monitoring of Salt bridges during simulation Run

g_saltbr? If you have salt bridges you already know about and want to look at, you can always go with g_dist per pair manually. On 2012-04-05 12:23:02PM +0400, James Starlight wrote: > Dear Gromacs Users! > > > I'd like to monitor origin and destabilisation of salt-bridges during > simulation t

Re: [gmx-users] how to change the timestamp of a xtc file

trjcat -settime or trjconv -t0 On 2012-04-05 03:59:44PM +0800, lina wrote: > Hi, > > A quick question, how can I change the .xtc file which beginning at 0, > end at 1 ns to beginning at 5ns and end at 6ns. > > Thanks for any suggestions, > > Best regards, > -- > gmx-users mailing listgmx-u

Re: [gmx-users] how to change the timestamp of a xtc file

On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai wrote: > trjcat -settime or trjconv -t0 Thank you, a further question, a trjcat-ed xtc file, which timestamp like 0-5 0-2 0-5 0-3 ... Are there someway to update them all in the trjcated ones? Thanks ahead, > > On 2012-04-05 03:59:44PM +0800, lina

Re: [gmx-users] which xtc file should be used for the trjconv command

On Thu, Apr 5, 2012 at 11:50 AM, Acoot Brett wrote: > Dear All, > > In the on-line tutorial on lysozyme > (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html), > there is a command > > trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -u

Re: [gmx-users] Monitoring of Salt bridges during simulation Run

Bharat, Peter thanks for advises I've checked g_saltbr but not found possible definition of the specified regions ( this utility lacks -n index.ndx option). How I could ignore contacts between solvent and protein ? Also what is the real *-t value should I provide ? As I understood this is only Rm

[gmx-users] on the MD extension command

Dear All,   I have tried the MD command extension for several times, but for the series of *.xvg curve analysis, it always comes from the time which the extension starts, rather than the time where the original MD starts.   In order to decide whether we need to initiate the extension, we need do

[gmx-users] something about tpr file

Hi, suppose I lost original .tpr file, can I get tpr file from the .xtc file ? I mean from the .xtc or trr file, not by re-run grompp to generate tpr file. Thanks ahead, Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] how to change the timestamp of a xtc file

On 05/04/12, lina wrote: > On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai wrote: > > trjcat -settime or trjconv -t0 > > Thank you, a further question, a trjcat-ed xtc file, which timestamp like > > 0-5 0-2 0-5 0-3 ... > > Are there someway to update them all in the trjcated ones? I've n

Re: [gmx-users] how to change the timestamp of a xtc file

On Thu, Apr 5, 2012 at 6:07 PM, Mark Abraham wrote: > > > On 05/04/12, lina wrote: > > On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai wrote: >> trjcat -settime or trjconv -t0 > > Thank you, a further question, a trjcat-ed  xtc file, which timestamp like > > 0-5 0-2 0-5 0-3 ... > > Are there somewa

Re: [gmx-users] Re: do_dssp

On 05/04/12, bharat gupta wrote: > Ok now after downloading the latest version of dssp, This won't work, because the latest version of DSSP is newer than any released version of GROMACS, and they made big changes. This was discussed at length on the list only yesterday... go and find tha

Re: [gmx-users] something about tpr file

On 05/04/12, lina wrote: > > Hi, > > suppose I lost original .tpr file, > > can I get tpr file from the .xtc file ? I mean from the .xtc or trr > file, not by re-run grompp to generate tpr file. > > No Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.or

Re: [gmx-users] how to change the timestamp of a xtc file

On 05/04/12, lina wrote: > On Thu, Apr 5, 2012 at 6:07 PM, Mark Abraham wrote: > > > > > > On 05/04/12, lina wrote: > > > > On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai wrote: > >> trjcat -settime or trjconv -t0 > > > > Thank you, a further question, a trjcat-ed xtc file, which timestamp

Re: [gmx-users] Atom N not found....

rama david wrote: Hi Gromacs friends, When I given the command ... pdb2gmx -f .. -o .. -p .. -ignh I gate the following error.. -- Program pdb2gmx, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, line: 1070

Re: [gmx-users] Monitoring of Salt bridges during simulation Run

On 05/04/12, James Starlight wrote: > Bharat, Peter thanks for advises > > I've checked g_saltbr but not found possible definition of the specified > regions ( this utility lacks -n index.ndx option). How I could ignore > contacts between solvent and protein ? Use trjconv -n and tpbconv

[gmx-users] the different protonation state of HIS

Dear All,   For the different protonation state of HIS, what are there 3-letter code for GROMACS? And how about -SH and -S-S- codon? Or do you have a web link for me to read? Do we still have any other confusing amino acids?   I am looking forward to getting a reply from you.   Cheers,   Acoot--

Re: [gmx-users] Re: questions about Principal Component Analysis

Dear Tserk and the rest of GROMACS users, Last time I measured the cosine content of different time intervals from the PCs of the whole trajectory. This time I did PCA for each time interval and measured the cc which is the right way I suppose. Maisuradze et al., 2009 claim that a CC value below 0

Re: [gmx-users] the different protonation state of HIS

On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett wrote: > Dear All, > > For the different protonation state of HIS, what are there 3-letter code for > GROMACS? And how about -SH and -S-S- codon? Or do you have a web link for me > to read? Do we still have any other confusing amino acids? In pdb2gmx -h

Re: [gmx-users] how to change the timestamp of a xtc file

On 2012-04-05 06:18:34PM +0800, lina wrote: > On Thu, Apr 5, 2012 at 6:07 PM, Mark Abraham wrote: > > > > > > On 05/04/12, lina wrote: > > > > On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai wrote: > >> trjcat -settime or trjconv -t0 > > > > Thank you, a further question, a trjcat-ed  xtc file, whi

Re: [gmx-users] the different protonation state of HIS

On 2012-04-05 08:55:24PM +0800, lina wrote: > On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett wrote: > > Dear All, > > > > For the different protonation state of HIS, what are there 3-letter code for This is also somewhat forcefield dependent (and how you name the histidines in the PDB as well). > >

[gmx-users] the different protonation state of HIS

Dear All,   For pdb2gmx, we have -ignh. Does -ignh will always give the correct HIS format at pH 7?   Looking forward to getting your reply.   Cheers,   Acoot From: lina To: Acoot Brett ; Discussion list for GROMACS users Sent: Thursday, 5 April 2012 10:55

Re: [gmx-users] the different protonation state of HIS

Acoot Brett wrote: Dear All, For pdb2gmx, we have -ignh. Does -ignh will always give the correct HIS format at pH 7? Strictly speaking, the -ignh option doesn't have anything to do with HIS protonation, it simply ignores H atoms in the input. HIS protonation states are then determined

Re: [gmx-users] the different protonation state of HIS

On 2012-04-05 06:19:07AM -0700, Acoot Brett wrote: > Dear All, >   > For pdb2gmx, we have -ignh. Does -ignh will always give the correct HIS > format at pH 7? -ignh does not do what you think it does. -ignh ignores the original PDB's hydrogen coordinates. Picking the "correct" histidine protona

[gmx-users] jobs failed

Hello: I am using the following script to run Gromacs in cluster, but it failed: # @ job_name = bm # @ class = kdm-large # @ error = gromacs.info # @ output = gromacs.out # @ environment = COPY_ALL # @ wall_clock_limit = 10:00:00 # @ notification = error # @ job_type = bluegene # @ bg_size = 64

[gmx-users] Zn Coordination

Dear all, I am relatively new to GROMACS and MD in general. I have gone through various GROMACS tutorials and successfully run a couple of my own simulations but that are pretty simple, i.e. just single chain protein with standard amino acids in SPC/E, not requiring much expert knowledge. I am n

[gmx-users] g_hbond

Hello, How can I add chlorin atom as a acceptor in g_hbond. I am using Gromacs VERSION 4.0.7 NIlesh -- 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 befor

Re: [gmx-users] Zn Coordination

Thomas Grant wrote: Dear all, I am relatively new to GROMACS and MD in general. I have gone through various GROMACS tutorials and successfully run a couple of my own simulations but that are pretty simple, i.e. just single chain protein with standard amino acids in SPC/E, not requiring muc

Re: [gmx-users] g_hbond

Nilesh Dhumal wrote: Hello, How can I add chlorin atom as a acceptor in g_hbond. Either modify the source code (the search_acceptors routine in gmx_hbond.c) or make a dummy structure/topology that lists the Cl atoms as O. The program searches for acceptors by atom name only (O and/or N i

[gmx-users] Different results from identical tpr after MD

Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted

Re: [gmx-users] Different results from identical tpr after MD

bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further con

Re: [gmx-users] Different results from identical tpr after MD

Thanks for the reply. * *I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA

[gmx-users] Re: jobs failed

> Hello: >   I am using the following script to run Gromacs in cluster, but it failed: > > # @ job_name = bm > # @ class = kdm-large > # @ error = gromacs.info > # @ output = gromacs.out > # @ environment = COPY_ALL > # @ wall_clock_limit = 10:00:00 > # @ notification = error > # @ job_type = blueg

Re: [gmx-users] Different results from identical tpr after MD

Well you're really supposed to conduct multiple runs anyway. Remember, a single MD run over a period of time only samples 1 possible trajectory out of the ensemble of possible trajectories... On 2012-04-05 11:38:20PM +0530, bipin singh wrote: > Thanks for the reply. > * *I read the link. So, how

Re: [gmx-users] Different results from identical tpr after MD

That's an interesting philosophical question. In this case, you'll wind up with a 50 ns trajectory where each configuration is consistent with the thermodynamic ensemble you're approximating. That's as close a definition to "realistic" as I think is worth worrying about. You'd only need to worry

Re: [gmx-users] Different results from identical tpr after MD

But we hope finally no matter which trajectory, a stable protein conformation should be got! As for during the production MD, no significant energy change included.   I am looking forward to getting more feedback on this topic.   Acoot From: Peter C. Lai To:

Re: [gmx-users] jobs failed

On 2012-04-05 04:15:00PM +0200, Albert wrote: Your box is violent shrinking too much for the domain decomposition routines to handle. What ensemble and integrator are you running? If normal md, then are you trying to NPT before NVT equilibration? > Hello: >I am using the following script to r

Re: [gmx-users] Different results from identical tpr after MD

Here I want to talk on the time length of production MD.   I have a professor on computational biology. She said for MD only several ps is enough. I have the expereince to run production MD for several ns, and I have got stable conformation.   But I am sure for some protein system, even a 50 ns M

Re: [gmx-users] Different results from identical tpr after MD

Acoot Brett wrote: Here I want to talk on the time length of production MD. I have a professor on computational biology. She said for MD only several ps is enough. I have the expereince to run production MD for several ns, and I have got stable conformation. Several ps is insufficient f

Re: [gmx-users] Different results from identical tpr after MD

bipin singh wrote: Thanks for the reply. / /I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather

[gmx-users] Re: job failed

Hello: thank you very much for kind reply. I tried NVT before I produced NPT MD production. thank you very much -- 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_List

Re: [gmx-users] Different results from identical tpr after MD

Hi Justin,   Can you give me your definition of converged MD and unconverged MD?   Cheers,   Acoot From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Friday, 6 April 2012 4:41 AM Subject: Re: [gmx-users] Different results from identical tpr af

[gmx-users] Re: job failed

On 2012-04-05 08:51:05PM +0200, Albert wrote: > Hello: >thank you very much for kind reply. >I tried NVT before I produced NPT MD production. > > thank you very much What pressure coupling barostat are you using? (pcoupl) -- ==

Re: [gmx-users] Re: job failed

Peter C. Lai wrote: On 2012-04-05 08:51:05PM +0200, Albert wrote: Hello: thank you very much for kind reply. I tried NVT before I produced NPT MD production. thank you very much What pressure coupling barostat are you using? (pcoupl) A full .mdp file and description of the syst

Re: [gmx-users] Different results from identical tpr after MD

Acoot Brett wrote: Hi Justin, Can you give me your definition of converged MD and unconverged MD? One could fill many textbook chapters with an answer to this question. Suffice it to say that one would consider a simulation converged if the properties of interest have also converged ar

[gmx-users] Help: Anyone worked with "Wall"?

Dear all, I'm trying to simulate with pbc=xy and I need two walls. My settings are as follows: pbc = xy nwall = 2 wall_atomtype = C C wall_type = 9-3 wall_r_linpot = -1 -1 wall_density= 20 20 wall_ewald_zfac = 3 The problem i

Re: [gmx-users] Help: Anyone worked with "Wall"?

For walls, the atoms in the wall are virtual. Remember that 9-3 LJ integratees over the volume behind the wall so you will have to set your atom density appropriately. Setting wall_density to 20/nm^3 for 9-3 wall leads to 20 carbon atoms per nm^3. That's not going to be totally solid, imo. I am

Re: [gmx-users] Re: questions about Principal Component Analysis

Hi Thomas, First of all, proteins in solution don't suddenly stop with Brownian motion at some point. It's just the way things move at the microscopic level. Second, the cosine content has nothing to do with randomness. Really. Nothing. On the contrary. The cosine content indicates unidirectional

[gmx-users] epsilon_r vs. gb_epsilon_solvent

Hi, all, I have a question regarding epsilon_r value. Do I have to specify the value in .mdp file? What is the default value if I do not specify it? If I use implicit solvent, there is one parameter: gb_epsilon_solvent, which is recommended to be 80 in the manual. What is the difference between g

[gmx-users] on the attachment symbol of some e-mail from our GROMACS users

Dear All,   Have you paid attention to this fact, for some e-mails from our Discussion list for GROMACS users, although they do not contain attachment files, the attachment file symbols exist.   What is the reason?   Cheers,   Acoot   -- gmx-users mailing listgmx-users@gromacs.org http://lis

[gmx-users] further discussion on the mdrun -append function

  Dear All,   Frim mdrun -h, I got the following message:     -[no]append bool yes Append to previous output files when continuing from checkpoint instead of adding the simulation art number to all file names     Thus there is the possibility that the series xvg curves can never starts from

Re: [gmx-users] Different results from identical tpr after MD

The following manuscript may be of interest. http://arxiv.org/abs/math/0610124v2 -Robert McGibbon On Apr 5, 2012, at 11:26 AM, Acoot Brett wrote: > But we hope finally no matter which trajectory, a stable protein conformation > should be got! As for during the production MD, no significant ene

Re: [gmx-users] further discussion on the mdrun -append function

On 6/04/2012 1:41 PM, Acoot Brett wrote: Dear All, Frim mdrun -h, I got the following message: /-[no]append bool yes Append to previous output files when continuing from checkpoint instead of adding the simulation art number to all file names/ Thus there is the possibility that the series xvg c

Re: [gmx-users] further discussion on the mdrun -append function

Sounds like there is a lanugage barrier? Anyway, some cluster filesystems don't support append (e.g. lustre). So I never use append. I will use tpbconv -extend and -o to a *different* tpr file, then run mdrun -deffnm new_extended which generates everything with the new_extended filename prefix.

Re: [gmx-users] further discussion on the mdrun -append function

Thanks for the detailed explaination.   Will you please explain the function of "-n index.ndx " in "grompp -f md.mdp -n index.ndx -p topol.top -c minimized.gro -o md-1ns.tpr" with some specific examples?   Cheers,   Acoot From: Peter C. Lai To: Discussion li

Re: [gmx-users] further discussion on the mdrun -append function

I sometimes use non-standard index groups in my .mdp. If you only reference the moleculetypes and/or Protein or Non-protein in your .mdp then you don't need a special index.ndx and the -n option becomes optional. Example: I specialize in membrane proteins. In my .mdp I have: tc-grps = Pr

[gmx-users] further discussion on the mdrun -append function

Dear Acoot: You should be able to answer this one yourself. Moreover, you are doing yourself a disservice by relying on the mailing list to do your work for you because you will eventually need to learn how to find answers to these things on your own. Please remember the following: 1. us

[gmx-users] Different results from identical tpr after MD

Dear Acoot: The idea of convergence is this: start a large number of simulations from different conformations, analyze some quantity over time in each simulation, and when the deviation of the average value of that quantity from each separate simulation is less than the time-variance with

Re: [gmx-users] further discussion on the mdrun -append function

On Fri, Apr 6, 2012 at 12:24 AM, Peter C. Lai wrote: > Sounds like there is a lanugage barrier? > > Anyway, some cluster filesystems don't support append (e.g. lustre). > I often use append on lustre. No problem. Why do you think it doesn't work? > > So I never use append. > > I will use tpbco

Re: [gmx-users] Re: job failed

hello: thank you very much for your kind messages. I first did minimization, the NVP with gradually heating the system from 0-310K, and them NPT production: NVT.mpd--- define = -DPOSRES -DPOSRES_LIG constraints= hbonds integrator= md dt= 0.001 ; ps !

Re: [gmx-users] Re: job failed

On 6/04/2012 3:36 PM, Albert wrote: hello: thank you very much for your kind messages. I first did minimization, the NVP with gradually heating the system from 0-310K, and them NPT production: NVT.mpd--- define = -DPOSRES -DPOSRES_LIG constraints= hbonds integr

[gmx-users] Does electric field be screened by the water ?

Dear gmx users: I would like to apply electric field to my simulation box, and I have added these to my input file: ; Format is number of terms (int) and for all terms an amplitude (real) = ; and a phase angle (real) = E_x = 1.0 0.71e-2 0 What I want to know is whether the size of

Re: [gmx-users] further discussion on the mdrun -append function

On 2012-04-06 01:30:20AM -0400, Roland Schulz wrote: > On Fri, Apr 6, 2012 at 12:24 AM, Peter C. Lai wrote: > > > Sounds like there is a lanugage barrier? > > > > Anyway, some cluster filesystems don't support append (e.g. lustre). > > > > I often use append on lustre. No problem. Why do you thi

Re: [gmx-users] Different results from identical tpr after MD

Yes you are right, that we need to do multiple MD runs before making any conclusion based on single trajectory. But I have not found any single research paper which discuss about conclusions drawn based on ensemble of trajectories. If you have any such research article then please send me the link.

Re: [gmx-users] something about tpr file

Hi Lina, The xtc/trr files do not contain information about atom names and residues. But surely you have a matching pdb/gro file somewhere? Cheers, Tsjerk On Apr 5, 2012 12:32 PM, "Mark Abraham" wrote: On 05/04/12, lina wrote: > > Hi, > > suppose I lost original .tpr file... No Mark --

Re: [gmx-users] Different results from identical tpr after MD

Thanks for your valuable suggestions. I am totally agree with your views. On Fri, Apr 6, 2012 at 00:11, Justin A. Lemkul wrote: > > > bipin singh wrote: > >> Thanks for the reply. >> / /I read the link. So, how one can predict something reliable using >> these results(based on 50ns in my case) w

Re: [gmx-users] Different results from identical tpr after MD

On 6/04/2012 3:53 PM, bipin singh wrote: Yes you are right, that we need to do multiple MD runs before making any conclusion based on single trajectory. But I have not found any single research paper which discuss about conclusions drawn based on ensemble of trajectories. If you have any such r

Re: [gmx-users] Does electric field be screened by the water ?

Op 6 apr 2012 om 07:44 heeft "Xianwei Wang" het volgende geschreven: > Dear gmx users: > I would like to apply electric field to my simulation box, and I have > added these to my input file: > ; Format is number of terms (int) and for all terms an amplitude (real) = > ; and a phase angle

[gmx-users] the g_rms function after we trjcat the trajectory files before and after extension

Dear All,   Before and after extention we have 2 trajectorty files, and by trjcat we got we, then we can do the g_rms   g_rms -s *.tpr -f *_noPBC.xtc -o rmsd.xvg -tu ns   But here for the g_rms command I find no matter whether we use the  *.tpr of the initiation of the production MD, or the *.tpr