Re: Re: [gmx-users] density of the bilayer

minnale [EMAIL PROTECTED] wrote: Hi users, Intially I have run the simulation of the bilayer for 5ns then extended this to 20ns. When analyse density of the bilayer by considering trajectories of these different timings one at 5ns.xtc anonther at 20ns.xtc its showing almost same density

[gmx-users] density of the bilayer

Hi users, Intially I have run the simulation of the bilayer for 5ns then extended this to 20ns. When analyse density of the bilayer by considering trajectories of these different timings one at 5ns.xtc anonther at 20ns.xtc its showing almost same density values how come it is possible? the

[gmx-users] Re:density of the bilayer

Thanks alot for your reply In case of water density, starting of the water density will be for some time should come straight line in the graph later gradually reducing and goes to zero towards centre of the bilayer again it increases and stop going the water density. but in my case

[gmx-users] centre of the system: error

Hi all, I am trying to make centre of the bilayer so I used following command line trjconv -f 20nspopc.xtc -centre rect -o 20nstrjout.xtc -n water.ndx based on http://www.gromacs.org/pipermail/gmx-users/2003-June/005995.html here I selected 3 (solution) again 3 (solution) for output of the

[gmx-users] g_potential

Hi, I have small doubt that when we calculate elctrostaic potenitial of POPC ,get system with neutral, POPC positive and water negative values, what is the reason behind that POPC has positive and water has negative values. water has H+ ion and OH- ion it should be neutral but why negative

[gmx-users] g_density?

  Hi all, I have small doubt on g_density, The bilayer thickness can be estimated by calculating density profile here I have calculated density for different groups in lipid system by g_density command. The POPC density profile x-axis(z-nm) vs y-axis(density), it looks M shape what

Re: Re: [gmx-users] g_density?

Thanks Justin for your response just glance below Hi all, I have small doubt on g_density, The bilayer thickness can be estimated by calculating density profile here I have calculated density for different groups in lipid system by g_density command. The POPC density profile

[gmx-users] Is there any realation between structure and RMSD?

Hi all I have simulated two systems(mutated and unmutated)of protein for 7ns and I plotted RMSD. here my doubt is that when I see these structures(superimpose)in VMD mutated final simulated structure with respective initial one drastic changes(means helix-coil and Beta-alpha transitions) but

[gmx-users] RMSD

Hi users, I have run two systems of protein simulation for 7ns, the difference between these systems change in the few resdues. After that I have done RMSD analysis. When I superimposed these two 7ns protein simulation systems with crystal structure seperately,I noticed that in one

[gmx-users] Gromacs 3.3.1. and 3.3.3

Hi Users, I have run protein system till 25ns in gromacs version 3.3.1 in dual processor system. Now I want to run new systems in cluster with gromacs version 3.3.3, in two cases the protein system is same but difference in few residues, If run new system in cluster compare the results

[gmx-users] personal com(Gromacs, v-3.3.1) and Cluster(Gromacs, v-3.3.3)?

Hi Users, I already simulated a protein system for 25ns in personal computer has gromacs version 3.3.1. Later I have started same protein system but few changes in few residues compare with earlier system. Due to the huge system and moreover I need to run three more systems( total four)

[gmx-users] PR after minimisation and PR of missing residues?

Hi all, I have two doubts on PR, may be these are trivial to you. 1.According to Gromacs procedure(from Gromacs tutorial) the sequential steps are (a)Energy minimisation (b)Position restrain with force constant descendant manner and finally (c)production. Here my doubt that, is it require to

[gmx-users] Re:Restarting problem of tpbconv

are incomplete, so just choose a frame present in both the .trr and .edr that is complete. Then you can use tpbconv -time with that timepoint. -Justin Thanks in advance. On Sat, 27 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Hi all My system was crashed inbetween simulation

[gmx-users] Restarting problem of tpbconv

Hi all My system was crashed inbetween simulation, so restarted the run by using tpbconv command tpbconv -f popc.trr -e popc.edr -s popc.tpr -o popc_restart -time 2235.2 -until 3000 it showing Last frame read 6173 WARNING: Incomplete frame: nr 6174 time

Re: [gmx-users] Restarting problem of tpbconv

6170 time 2234.000 gcq#85: All Beauty Must Die (Nick Cave) Any suggestions would be appreciated Thanks in advance. On Sat, 27 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Hi all My system was crashed inbetween simulation, so restarted the run by using tpbconv command tpbconv -f

[gmx-users] Question regarding Gromacs

Hi all , I am having general doubts regaring GROMACS those are unclear me writing you 1. If a system contain equal number of atoms run these systems in GROMACS and in AMBER why former one simulates faster than second one? 2.If do minisation while running shows that Back Off! I just backed

[gmx-users] Re:Question regarding Gromacs

I am having general doubts regaring GROMACS those are unclear me writing you 1. If a system contain equal number of atoms run these systems in GROMACS and in AMBER why former one simulates faster than second one? Because GROMACS is a great software. Thanks for the reply, what may

[gmx-users] Re:Leaflet of Bilayer

Thanks alot to Chris and Alan for given their valuable suggestions then a small doubt about time length of bilayer simulation, that is if I concentrate mainly on protein but not on membrane is it require to run =50ns or 20ns of POPC alone before inserting protein into it. Earlier I

Re: Re: [gmx-users] Re: Leaflet of Bilayer

, but that is for capping the amount of water molecules added to a box. -Justin Could you suggest me Thanks in advance. On Fri, 19 Sep 2008 Jochen Hub wrote : minnale wrote: Hi all, I have extended popc bilayer(intial popc.pdb from Dr.Tielmen site

[gmx-users] Leaflet of Bilayer

Hi all, I have extended popc bilayer(intial popc.pdb from Dr.Tielmen site) by using genbox command, I issued genbox -cs popc128a.gro -o out.gro -box 9.2 9.2 6.9 it ran successfully with increase of popc and water molecules. Now I want to visualise this out file in VMD in a way that in

Re: Re: [gmx-users] Leaflet of Bilayer

molecules. 1.Is it wrong if I increase the popc molecules by using genbox? 2.Is there anyway to increase popc and water numbers by mentioning specific molecules number? Could you suggest me Thanks in advance. On Fri, 19 Sep 2008 Jochen Hub wrote : minnale wrote: Hi all, I have extended

[gmx-users] Re: Leaflet of Bilayer

of. There is a -maxsol option in genbox, but that is for capping the amount of water molecules added to a box. -Justin Could you suggest me Thanks in advance. On Fri, 19 Sep 2008 Jochen Hub wrote : minnale wrote: Hi all, I have extended popc bilayer(intial popc.pdb

[gmx-users] Re:GROMACS sample procedure

Hi, Its good to chose Gromacs for running MDSimulations. Gromacs procedure cocern many tutorials are available in the net just type gromacs tutorials in google moreover check the gmx-archives regularly for finding solutions corresponding queries. Good luck. I am new to GROMACS

Re: Re: [gmx-users] Position restrain of protein and membrane

of badcontacts, for that require to keep PR on POPC, so it can relieve badcontacts and get minimised structure. am I right? On Tue, 16 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks for reply Justin, can I do this way first I will keep PR on popc later protein, I dont want keep PR

Re: Re: [gmx-users] Position restrain of protein and membrane

of badcontacts, for that require to keep PR on POPC, so it can relieve badcontacts and get minimised structure. am I right? On Tue, 16 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks for reply Justin, can I do this way first I will keep PR on popc later protein, I dont want keep PR

Re: Re: [gmx-users] Position restrain of protein and membrane

Thanks for reply Justin, can I do this way first I will keep PR on popc later protein, I dont want keep PR on water.Can I do like this? Thanks in advance. On Tue, 16 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks Justin for your kind reply, you misunderstood my query,now I am asking

Re: Re: [gmx-users] Position restrain of protein and membrane

change according to ourselves. I hope you understood my problem. Can you give me suggestion Thanks in advance. minnale wrote: Hi all, I embedded protein into popc bilayer by using genbox command, in equilibration I want keep restrain only on protein but not on popc? can I do like

Re: Re: [gmx-users] extracting specfic trajectories?

or wrong? Thanks alot for any suggestion. On Sat, 13 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Hi all, I have run the simulation with 100 steps interval in .log file till 5ns, now I want to extract the new trajectory file should conatin with 1000 steps inerval trajectories excluding

[gmx-users] g_hbond getting abnormal graph

Hi all, I have issued the command of g_hbond like this g_hbond -f .xtc -s .tpr -n .ndx -num .xvg -hbm.map -a 30 while finishing of this command, it told 1 H-bond found and run successfully. When I plotted .xvg file by using gnuplot its showed zigzag manner graph(abnormal) and I never got this

Re: Re: Re: [gmx-users] g_hbond getting abnormal graph

in .xvg format. Could you open in xmgrace and suggest me whether what I have done is correct or not. Thanks in advance. On Thu, 11 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Hi all, I have issued the command of g_hbond like this g_hbond -f .xtc -s .tpr -n .ndx -num .xvg -hbm.map

[gmx-users] regarding xpm2ps?

I have converted .xpm (which generated from *g_hbond) to .eps by using xpm2ps command, after finished the running of this command showed There are 1 matrices in .xpm Matrix 0 is 37501 x 1 Auto tick spacing failed for X-axis, guessing 2 Auto tick spacing for X-axis: major 2, minor 0.4 Auto

Re: Re: [gmx-users] regarding xpm2ps?

Thanks alot On Wed, 10 Sep 2008 Justin A.Lemkul wrote : minnale wrote: I have converted .xpm (which generated from *g_hbond) to .eps by using xpm2ps command, after finished the running of this command showed There are 1 matrices in .xpm Matrix 0 is 37501 x 1 Auto tick spacing failed for X-axis

Re: Re: [gmx-users] regarding xpm2ps?

variable) Could please tell me how can I remedy this problem? Thanks alot On Wed, 10 Sep 2008 Justin A.Lemkul wrote : minnale wrote: I have issued the following command xpm2s -f .xpm -o .eps If I mention option -di with m2p it showed Fatal error: Library file H_hbond.m2p not found in current dir

Re: Re: [gmx-users] sn1 and sn2 chains of popc

Thanks alot Justin for your detailed explanation. On Mon, 08 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks Justin for your reply you mean to say that C32 of glycerol involves in the palimotyl chain formation so call as sn1 chain similarly C12,C13 of glycerol involves in the oleyl

[gmx-users] (no subject)

Hi all, I am interested about analyse some of the results with amber and gromacs md packages. Could anyone tell me how to convert .xtc of gromacs to trajectory input for amber. eagerly waiting for reply Thanks in advance.___ gmx-users mailing list

[gmx-users] conversion?

Hi all, I am interested about analyse some of the results with amber and gromacs md packages. Could anyone tell me how to convert .xtc of gromacs to trajectory input for amber. eagerly waiting for reply Thanks in advance.___ gmx-users mailing list

Re: Re: [gmx-users] conversion?

thanks alot Justin for your reply On Tue, 09 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Hi all, I am interested about analyse some of the results with amber and gromacs md packages. Could anyone tell me how to convert .xtc of gromacs to trajectory input for amber. eagerly

[gmx-users] g_dist

Hi all, I want to calculate distance of protein residues by using g_dist, now I have doubt that 1.Is it possible to calculate distance for more than two residues of two comparable systems? 2. which type of group select for generating index

[gmx-users] sn1 and sn2 chains of popc

Hi all, may be this is very basic query I want to calculate order parameters of popc. I have found in archives that make sn1.ndx(pamitoyl) and sn2.ndx(oleyl) of popc then feed these files to g_order command. Can anyone tell me that why pamitoyl call as sn1 and oleyl call as sn2? Thanks for

Re: Re: [gmx-users] sn1 and sn2 chains of popc

: minnale wrote: Hi all, may be this is very basic query I want to calculate order parameters of popc. I have found in archives that make sn1.ndx(pamitoyl) and sn2.ndx(oleyl) of popc then feed these files to g_order command. Can anyone tell me that why pamitoyl call as sn1 and oleyl call as sn2

[gmx-users] Couldnt get log file for g_hbnd command

Hi all, I had gromacs version 3.3.1 later I have installed very recent version 3.3.3 then I have given command like this *g_hbond -f .xtc -s .tpr -n .ndx -num .xvg -hbm .xpm -g .log whatever I have mentioned output files generated except .log file Can you tell what could be the reason?

Re: Re: [gmx-users] how to make h-bond existence map?

Sep 2008 Florian Haberl wrote : Hi, On Wednesday, 3. September 2008, minnale wrote: Thanks Justin for your valuable suggestions I have done the way you suggested. I gave command like this g_hbond -f .xtc -s .tpr .ndx(contain 5 residues mainchain+H 25 atoms) -num .xvg -hbm .xpm it showed

Re: Re: [gmx-users] how to make h-bond existence map?

in advance On Wed, 03 Sep 2008 Florian Haberl wrote : Hi, On Wednesday, 3. September 2008, minnale wrote: Thanks Florian for your detailed reply when I mentioned -r and -a options in g_hbond command its showing Fatal error: Expected a real argument for option -a similar error showing when

[gmx-users] how to make h-bond existence map?

Hi all, I am confusing while calculating hydrogen bonds of my protein.I issued this command g_hbond -f .xtc -s .tpr -num .xvg I didnt mention .ndx because I wanted to know the H-bonds in whole protein system. I have selected mainchain+H two times, command went fine and it showed Select

Re: Re: [gmx-users] how to make h-bond existence map?

to convert .xpm to .eps by using command xpm2ps -f .xpm -o .eps it showed Floating point exception Can you please give me your kind suggestion Thanks in advance. On Wed, 03 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Hi all, I am confusing while calculating hydrogen bonds of my protein.I

[gmx-users] Understanding of POPC analysis

Hi all, this may be trivial question to you. I am unfamiliar with gromacs. My doubt is that in POPC analysis most of the cases concerning about Z-axis why not X and Y. Can you please clear me this doubt. Thanks in advance for your suggestion.

[gmx-users] Potential energy of POPC

Hi all, I have done popc simulation for 5ns and calculated potential energy of POPC. The values started from -269000 kj/mol reduced to -272000 kj/mol. Could you please tell me 1.is it require to extend my simulation from 5ns? 2. The above mentioned potential energy values whether correct

[gmx-users] Re: gmx-users Digest, Vol 52, Issue 118

: [gmx-users] g_hbond + invalid command line argument -g (minnale ) 2. a question about the content in atm-pair.out file (Cao, Yang) 3. about connections (ravi sharma) 4. Re: g_hbond + invalid command line argument -g (David van der Spoel

[gmx-users] g_hbond + invalid command line argument -g

Hi all, I am new to gromacs, I am interested in calculate Hydrogen bonds of my protein. So I have issued the *g_hbond command like this g_hbond -f .xtc -s .tpr -n .ndx(Index file contain all residues mainchain+H atoms) -num .xvg -g .log its showed Program g_hbond, VERSION 3.3.1 Source

Re: Re: [gmx-users] g_hbond + invalid command line argument -g

690 1.2 81 700 1.4 75 681 1.6 83 687 the first column is time then could please tell about 2nd and 3rd columns Thanks in advance. On Thu, 28 Aug 2008 Justin A.Lemkul wrote : minnale wrote: Hi all, I am new

Re: Re: [gmx-users] g_hbond + invalid command line argument -g

690 1.2 81 700 1.4 75 681 1.6 83 687 the first column is time then could please tell about 2nd and 3rd columns Thanks in advance. On Thu, 28 Aug 2008 Justin A.Lemkul wrote : minnale wrote: Hi all, I am new

Re: Re: [gmx-users] g_hbond + invalid command line argument -g

A.Lemkul wrote : minnale wrote: Thanks Justin for your quick reply the g_hbond command ran succesfully and gave me .xvg file and it contain 3 columns that is like @title Hydrogen Bonds @xaxis label Time @yaxis label Number @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend

[gmx-users] Re: gmx-users Digest, Vol 52, Issue 66

in the same directory (/usr/local/bin), and everything is just work fine. Nuno Azoia Justin A. Lemkul wrote: minnale wrote: Thanks for the reply Justin I tried like this do_dssp -f .xtc -s .tpr -n .ndx -map str.map -o str it has given Fatal error: DSSP executable (/usr/local/bin

Re: Re: [gmx-users] problem with protein secondary structure analysis

= isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 Couls you please tell me how can I select subset of my trajectory file. May be this is simple question. Thanks in advance. Hi Minnale, We do appreciate that english is not your

Re: Re: [gmx-users] problem with protein secondary structure analysis

= isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 Couls you please tell me how can I select subset of my trajectory file. May be this is simple question. Thanks in advance. Hi Minnale, We do appreciate that english is not your

Re: RE: Re: [gmx-users] problem with protein secondary structure analysis

PROTECTED] On Behalf Of minnale Sent: Sunday, August 17, 2008 08:30 AM To: gmx-users1 Subject: Re: Re: [gmx-users] problem with protein secondary structure analysis Thanks to Justin for his prompt reply in .mdp file mentioned energy groups and tc-grps are protein and sol_cl . I am in doubt

[gmx-users] problem with protein secondary structure analysis

Hi all, I intersted in analysing secondary structure of protein by using VMD and performed these steps. 1. First loaded min.gro file and corresponding min.xtc then all equalibration .xtc files till here MD movie has run fine. 2. I had long trajectory in a single file, so cut it down

Re: Re: [gmx-users] problem with protein secondary structure analysis

it. one more doubt I am having is If I load entire .xtc file which contain 7ns trajectory it didnt load Could please tell me why its not loading Thanks in advance. On Sat, 16 Aug 2008 Justin A.Lemkul wrote : minnale wrote: Hi all, I intersted in analysing secondary structure of protein

[gmx-users] do_dssp

Hi all, I want to analyse secondary struture of my protein which have run MD for 7ns. I have checked in archives about do_dssp, found that can use only .pdb file instead of .trr and .tpr. Then if type command with -h it has it has given .xtc, .tpr, and .ndx should use. I am bit confusing

Re: Re: [gmx-users] do_dssp

imagine that reading the full-precision trajectory will slow to an absolute crawl. -Justin Justin A. Lemkul wrote: minnale wrote: Hi all, I want to analyse secondary struture of my protein which have run MD for 7ns. I have checked in archives about do_dssp, found that can use only .pdb

[gmx-users] Re: gmx-users Digest, Vol 52, Issue 5

Thanks Justin for your promt reply, whatever you told is correct, with same .xtc , .tpr , .ndx files I have used in gromacs version 3.3 It is working. Thanks alot once again. minnale wrote: Thanks to Justin for his suggestion I tried the way mentioned in http://wiki.gromacs.org

[gmx-users] Order parameters of lipid

I want to calculate order parameters of palmitoyl and oleyl chains of POPC which ran it for 5ns, so I have done below mentioned steps. 1. First I tried for Palmitoyl, so I made .ndx file by using make_ndx command and selected a C34|a 035|a C36.a C50. In index file the palmitoyl chain

Re: Re: [gmx-users] Order parameters of lipid

Jul 2008 Justin A.Lemkul wrote : minnale wrote: I want to calculate order parameters of palmitoyl and oleyl chains of POPC which ran it for 5ns, so I have done below mentioned steps. 1. First I tried for Palmitoyl, so I made .ndx file by using make_ndx command and selected a C34|a 035|a C36

[gmx-users] doesn't match coordinate file with topology

Hi users, I have generated .gro file of protein by using .xtc file with trjconv command after that i used pdb2gmx command for generating topology file without any error. when I have inserted this protein into popc bilayer by using genbox command i has deleted some of the water and popc

Re: Re: [gmx-users] doesn't match coordinate file with topology

Thank you Peyman On Thu, 24 Jul 2008 Peyman Yamin wrote : On Thursday 24 July 2008 09:46, minnale wrote: Hi users, I have generated .gro file of protein by using .xtc file with trjconv command after that i used pdb2gmx command for generating topology file without any error. when

[gmx-users] Doubt regarding popc simulations

Hi all, I want to ask one question regarding time of POPC simulations, this may be trivial query to you that is how long time normally popc alone simulations have to run? I know that if potential energy plot shows values from high to low which depicts stable graph we can stop the

Re: Re: [gmx-users] make_ndx problem

group. Could you please tell me which one use it for analysis if PO4 how select by using make_ndx? Thanks alot in advance. On Wed, 16 Jul 2008 Florian Haberl wrote : Hi, On Wednesday, 16. July 2008, minnale wrote: Hi Users, I want to do analysis of g_density of lipidbilayer so how can I select

Re: Re: [gmx-users] make_ndx problem

Thanks once again. Ideally I shouldnt do for whole system. Ok. On Wed, 16 Jul 2008 Justin A.Lemkul wrote : minnale wrote: but here I am calculating density for 128 lipids not for 64 lipids. Is it right what iam doing? The examples on the wiki are just a few illustrative ideas, meant

Re: Re: [gmx-users] Abnormal popc struture after inserting protein

Thanks alot Justin I will do it in the way you suggested. On Wed, 02 Jul 2008 Justin A.Lemkul wrote : minnale wrote: Thanks to Justin for comment about my problem I will tell you clearly 1. Initially POPC bilayer taken from Tieleman website and run the simulation for 5ns. 2. Protein

[gmx-users] Abnormal popc struture after inserting protein

Hi all, I have embedded protein into POPC bilayer, I accomplished energy minimisation em.mdp file cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 500 ; Energy minimizing stuff ;

[gmx-users] step size too small

Hi all, 1) I have embedded protein into popcbilayer 2) Energy minimisation 3) Later added ions by using genion, 4) When I am trying to run minimisation its showing following sentences Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested

[gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

HI users, I have embedded protein in popc bilayer and ran the minimisation succesfully , before going equilibration I would like to confirm one thing that how to run the equilibration with on which system keep position restrain? 1.we will keep position restrain on all the

[gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

HI users, I have embedded protein in popc bilayer and ran the minimisation succesfully , before going equilibration I would like to confirm one thing that how to run the equilibration with on which system keep position restrain? 1.we will keep position restrain on all the

Re: Re: [gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

On Sun, 29 Jun 2008 Justin A.Lemkul wrote : minnale wrote: HI users, I have embedded protein in popc bilayer and ran the minimisation succesfully , before going equilibration I would like to confirm one thing that how to run the equilibration with on which system keep position

Re: Re: [gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

On Sun, 29 Jun 2008 Justin A.Lemkul wrote : minnale wrote: HI users, I have embedded protein in popc bilayer and ran the minimisation succesfully , before going equilibration I would like to confirm one thing that how to run the equilibration with on which system keep position

Re: Re: [gmx-users] Doubt regarding position restrain of protein embedded in popc bilayer system

Thanks for your invaluable reply to Justin and syma. On Sun, 29 Jun 2008 Justin A.Lemkul wrote : minnale wrote: Thanks for your prompt reply, according to you for membrane protein protocols keep restrain only on protein but not on lipid and water, is there any possibility to move

[gmx-users] Magic number error

Hi Users, I have run the protein simulation for 9ns, with 1ns each time by using tpbconv *command, after converting all9ns .trr files to .xtc i have deleted all .trr files. Later I have catenated all the 9ns simulation files by using trjcat command. Now I want restart my simulation, so

[gmx-users] Understanding about the deleted trajectory file

Hi all, I want to know one thing that if delete .trr file, still job will be running (submitted job), where will go all these trajectories? Regarding .edr , .log the information will go to respective files by update. Can anyone tell that where trajectories will go, if those go

Re: Re: [gmx-users] Understanding about the deleted trajectory file

the .trr file where trjectory information will go? I hope you got it now. On Thu, 26 Jun 2008 Justin A.Lemkul wrote : minnale wrote: Hi all, I want to know one thing that if delete .trr file, still job will be running (submitted job), where will go all these trajectories? Regarding

[gmx-users] POPC structure

Hi all, I found 128 popc lipid molecules in prof Tieleman's website ,I want to work on lipids with more than 128 popc lipid molecules, I knew that with help of VMD generate popc lipid molecules how many number we want. Can anyone suggest anyother website. Thanks in advance.

[gmx-users] Retrieving .trr file?

Hi gmx users, I have deleted *.trr file by mistake, Can anyone tell is there anyway to retrive *.trr file, remaining all *.tpr *.edr *.gro *.log files there. Thanks in advance.___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Retrieving .trr file?

Thank you very much Tsjerk. Hi Minnale, You could've checked the archives. Searching on trr and deleted would have yielded (among others): http://www.gromacs.org/pipermail/gmx-users/2008-May/034217.html Tsjerk On Tue, Jun 24, 2008 at 5:40 AM, minnale minnale_gnos at rediffmail.com wrote

Re: Re: [gmx-users] Understanding the concept of area per lipid calculation

Jojart Balazs wrote : Dear Minnale, just a comment. Are you sure, that the APL value of POPC is about 0.63nm^2? Because, as far as I know, at 303K the APL is about 0.683nm^2. (Structure of fully hydrated fluid phase lipid bilayers with monounsaturated chains - Nagle et al.). Which temperature

[gmx-users] Seperation of specific trajectory from whole trajectory file.

Hi all, I have run the protein simulation for 7ns with time interval 1ns each time, after that I catenated all the trj files by using trjcat command. Now I want to separate the 1ns .xtc from 7ns trajectory, is it possible to recover the 1ns trajectory file from entire 7ns

[gmx-users] Time evolution of lipidbilayer

Hi all, This may be a trivial question I want to calculate time evolution of area per lipid The steps I have done are 1. Extracted BoxX and BoxY values of 5ns_popc.edr by using g_energy command. 2. I have written code for calculating area per lipid in way that boxX multiply with boxY

[gmx-users] Re:Time evolution of lipidbilayer

Content-type: multipart/alternative; boundary=Next_1213018572---0-202.137.237.238-31592 This is a multipart mime message --Next_1213018572---0-202.137.237.238-31592 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition:

Re: Re: [gmx-users] Re:Time evolution of lipidbilayer

Thanks for your prompt reply, Yes I will do further analysis a)thickness of bilayer b) g_order of popc by using 5ns trjectory file. Thank you On Mon, 09 Jun 2008 Justin A.Lemkul wrote : trjcat, then do your analysis. -Justin minnale wrote: Content-type: multipart/alternative

[gmx-users] problem about g_sas of POPC bilayer

Hi all, I have downloaded POPC bilayer from peter teileman,s website and simulated for 5ns under anisotropic pressure coupling. When I drew a potential energy plot its shown that system is stabilised, so I have stopped the simulation at 5ns. After that I have mentioned g_sas command

[gmx-users] Re: Re: problem about g_sas of POPC bilayer

Thanks for your reply NO, I am having 64 lipids in each leaflet of bilayer. I want to calculate average area per lipid. what I have mentioned options are correct for g_sas? Thanks for your appreciation innale wrote: Hi all, I have downloaded POPC bilayer from peter teileman,s

[gmx-users] (no subject)

Hi all, I ran protein simulation in water for 9ns and plotted RMSD but it didnt stabilize, iam doubting on steps what I have done I am mentioning the steps 1.EM in vaccum 2.PR in vaccum in NVT 3.EM in water 4.PR in water in NVT 5.Production run for 250 ps in NPT remain 9ns run in MVT

[gmx-users] g_rms: Too many iterations in routine JACOBI

Hi all, 1)I made make_ndx file for my protein because i want to plot rmsd for specific residues in protein, so I have givenlike this 1 r 50-80 2)Then I have used trjcat -f 1ns.xtc 2ns.xtc 3ns.xtc -n r_50_80.ndx -settime -o trjout , here I selected Protein__r_50-80 this command ran without

[gmx-users] Re: g_rms: Too many iterations in routine JACOBI

:18 AM, minnale minnale_gnos at rediffmail.com wrote: Hi all, 1)I made make_ndx file for my protein because i want to plot rmsd for specific residues in protein, so I have givenlike this 1 r 50-80 2)Then I have used trjcat -f 1ns.xtc 2ns.xtc 3ns.xtc -n r_50_80.ndx -settime -o trjout

[gmx-users] membrane stabilisation

Hi gmx-users, I want to know that how can you say membrane got steady state for insertion of protein into that? Incase of protein we can say that protein got stable based on RMSD plot by using c-alpha of all residues. Thanks for your invaluable suggestion,

[gmx-users] Understanding about OPLS-aa for lipids

Hi all, I am new to gromacs, I wanted to use OPLS-aa forcefield for both lipid and protein. I have checked in archives regarding this problem and found link. That means the steps given are opls-aa ff for lipid? or ffgmx ff for lipids are just changing parameters by adding sigma and epsilon

[gmx-users] Re:Understanding about OPLS-aa lipids

Thanks Mark for your reply, I wanted to ask you that, the link which I mentioned means opls-aa ff specifially for lipids? I wanted to use opls-ff for both protein and lipid , shall I follow the procedure according to the link.

[gmx-users] Unable to continue the simulation

Hi all, My system without velocities in md.mdp file crashed mid of the simulation due to disk full, so I have used *tpbconv command for continue the simulation but it showing following error when I use these command *tpbconv -f prt.trr -s prt.tpr -o out.tpr -e prt.edr Fatal error: Could not

[gmx-users] Position restrain of protein and membrane

color_url = "006792"; google_color_text = "00"; //--> [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx-users] Position restrain of protein and membrane minnale

[gmx-users] Position restrain of protein and membrane

_color_url = "006792"; google_color_text = "00"; //--> [gmx-users] Position restrain of protein and membrane minnale Re: [gmx-users] Position restrain of protein and membrane Justin A. Lemkul Re: Re: [gmx