Re: [gmx-users] protein near the edges of simulation box

Oh, Thanks a lot. That is really  kind of you.   Sincerely, Shima From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Friday, June 15, 2012 9:13 PM Subject: Re: [gmx-users] protein near the edges of simulation box On 6/15/12 12:41 PM, Shima

Re: [gmx-users] protein near the edges of simulation box

On 6/15/12 12:41 PM, Shima Arasteh wrote: Thanks. Sorry, what do you mean by trajectory A and B? It's just a generic example. To be absolutely clear, let's say you have a trajectory named "md.xtc" that mdrun produces. That trajectory will have molecules that diffuse all over the place. Y

Re: [gmx-users] protein near the edges of simulation box

Thanks. Sorry, what do you mean by trajectory A and B?   Sincerely, Shima From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Friday, June 15, 2012 9:04 PM Subject: Re: [gmx-users] protein near the edges of simulation box On 6/15/12 12:19 P

Re: [gmx-users] Simple question (confout)

On 6/15/12 12:11 PM, Dariush Mohammadyani wrote: Hi, Is there any difference between confout.gro file and last frame which we can extract from trajectory? I am thinking they are different!! When I see the trajectory I can see the edge of the well-shaped box, but when I see confout.gro it is not

Re: [gmx-users] protein near the edges of simulation box

On 6/15/12 12:19 PM, Shima Arasteh wrote: OK, but as I know the trjconv is a command after mdrun, so when I get the output of mdrun and see it in VMD, it doesn't make different. Now wondering what is the benefit of trjconv -center and -pbc? You have to load the output trajectory from trjc

Re: [gmx-users] protein near the edges of simulation box

 OK, but as I know the trjconv is a command after mdrun, so when I get the output of mdrun and see it in VMD, it doesn't make different. Now wondering what is the benefit of trjconv -center and -pbc? Sincerely, Shima From: Justin A. Lemkul To: Shima Araste

Re: [gmx-users] protein near the edges of simulation box

On Fri, Jun 15, 2012 at 5:46 PM, Shima Arasteh wrote: > Dear Elton, > Where am I supposed to use trjconv -center ? when I want to get the mdrun? > As Justin mentioned, you should use if after mdrun, on your .xtc (or.trr) files. Check the manual. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dep

[gmx-users] Simple question (confout)

Hi, Is there any difference between confout.gro file and last frame which we can extract from trajectory? I am thinking they are different!! When I see the trajectory I can see the edge of the well-shaped box, but when I see confout.gro it is not well-shaped and some atoms looks went out out of th

Re: [gmx-users] protein near the edges of simulation box

On 6/15/12 11:46 AM, Shima Arasteh wrote: Dear Elton, Where am I supposed to use trjconv -center ? when I want to get the mdrun? trjconv is a post-processing command that can be used for a variety of purposes, of which one of the more common ones is to transform coordinates for convenient v

Re: [gmx-users] protein near the edges of simulation box

Dear Elton, Where am I supposed to use trjconv -center ? when I want to get the mdrun?   Sincerely, Shima From: Elton Carvalho To: Discussion list for GROMACS users Sent: Friday, June 15, 2012 7:43 PM Subject: Re: [gmx-users] protein near the edges of simulat

Re: [gmx-users] protein near the edges of simulation box

Thanks.   Sincerely, Shima From: Elton Carvalho To: Discussion list for GROMACS users Sent: Friday, June 15, 2012 7:43 PM Subject: Re: [gmx-users] protein near the edges of simulation box On Fri, Jun 15, 2012 at 1:23 PM, Tsjerk Wassenaar wrote: > You can s

Re: [gmx-users] protein near the edges of simulation box

On Fri, Jun 15, 2012 at 1:23 PM, Tsjerk Wassenaar wrote: > You can specify the protein to have no net center of mass > motion, by setting it as comm_grps in the .mdp file. > If the user is just concerned about visualization, trjconv -center solves his problem. -- Elton Carvalho Tel.: +55 11 309

Re: [gmx-users] Numbering for pbc_atom0

Nevermind. I figured it out I think. It was more of a problem with box size. Erik 15 jun 2012 kl. 14.20 skrev Erik Marklund: > Hi users, > > I am seeing some unexpected behavior for my COM pulling simulations. Errors > arise from the COM and distance calculations and I reckon it can be fixed b

Re: [gmx-users] Tutorial KALP-15 in DPPC

Thanks, got it.   Sincerely, Shima From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Friday, June 15, 2012 7:07 PM Subject: Re: [gmx-users] Tutorial KALP-15 in DPPC On 6/15/12 10:34 AM, Shima Arasteh wrote: > >  Thanks for your reply. >

Re: [gmx-users] Tutorial KALP-15 in DPPC

On 6/15/12 10:34 AM, Shima Arasteh wrote: Thanks for your reply. But one more question: what about when the applied lipid bilayer is POPC? Is this .top file (topol_dppc) useful yet? How come? You know, my main problem is that I don't know where this .top file come from? It was created wit

Re: [gmx-users] Tutorial KALP-15 in DPPC

 Thanks for your reply. But one more question: what about when the applied lipid bilayer is POPC? Is this .top file (topol_dppc) useful yet? How come? You know, my main problem is that I don't know where this .top file come from? Sincerely, Shima From: Justi

Re: [gmx-users] Tutorial KALP-15 in DPPC

On 6/15/12 10:25 AM, Shima Arasteh wrote: Dear gmx users, I am doing KALP15 in DPPC following the Justin tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html . In the second step, the first command is grompp as follow: grompp -f mi

[gmx-users] Tutorial KALP-15 in DPPC

 Dear gmx users, I am doing KALP15 in DPPC following the Justin tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html . In the second step, the first command is grompp as follow:grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o e

Re: [gmx-users] problem regarding installation of gromacs-4.5.5

On 6/15/12 8:45 AM, Nidhi Jatana wrote: Dear Sir/Madam I checked up in the system, there was one version of gromacs in /opt/bio/. I removed that and I reinstalled gromacs using the following commands: tar -xvf gromacs-4.5.5.tar.gz cd gromacs-4.5.5 ./configure --program-suffix="_mpi" ma

Re: [gmx-users] problem regarding installation of gromacs-4.5.5

On 15/06/2012 10:45 PM, Nidhi Jatana wrote: Dear Sir/Madam I checked up in the system, there was one version of gromacs in /opt/bio/. I removed that and I reinstalled gromacs using the following commands: tar -xvf gromacs-4.5.5.tar.gz cd gromacs-4.5.5 ./configure --program-suffix="_mpi"

Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation [SOLVED]

On 15/06/12 13:02, Justin A. Lemkul wrote: In the existing code for version 4.5.5, it seems the "Andersen" keyword is accepted but there is no mention of its use in update.c or coupling.c, suggesting to me that it's a ghost parameter that does nothing. There should be some indication in the .log

Re: [gmx-users] simulation box shape and length

On 6/15/12 8:47 AM, tarak karmakar wrote: Dear All, I am little unaware of choosing the shape and length of box while simulating protein in water. I saw in one of the GROMACS tutorials [ http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water] in which they have kept the

[gmx-users] simulation box shape and length

Dear All, I am little unaware of choosing the shape and length of box while simulating protein in water. I saw in one of the GROMACS tutorials [ http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water] in which they have kept the protein at the center of the box and the dista

Re: [gmx-users] problem regarding installation of gromacs-4.5.5

Dear Sir/Madam I checked up in the system, there was one version of gromacs in /opt/bio/. I removed that and I reinstalled gromacs using the following commands: tar -xvf gromacs-4.5.5.tar.gz cd gromacs-4.5.5 ./configure --program-suffix="_mpi" make make mdrun -j 8 make install make inst

[gmx-users] Numbering for pbc_atom0

Hi users, I am seeing some unexpected behavior for my COM pulling simulations. Errors arise from the COM and distance calculations and I reckon it can be fixed by increasing the box size and/or choosing good atoms as pbc_atomX in the mdp file. From the documentation it's not clear to me if it's

Re: [gmx-users] problem regarding installation of gromacs-4.5.5

On 6/15/12 7:37 AM, Nidhi Jatana wrote: Dear Sir/Madam This is Nidhi Jatana. I downloaded the lastest version of gromacs i.e. 4.5.5 from the link (ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz) and have installed it but whenever I am trying to run any of the programs, its showing me th

[gmx-users] problem regarding installation of gromacs-4.5.5

Dear Sir/Madam This is Nidhi Jatana. I downloaded the lastest version of gromacs i.e. 4.5.5 from the link (ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz) and have installed it but whenever I am trying to run any of the programs, its showing me the version to be 4.0.5. For example, I was tr

Re: [gmx-users] protein near the edges of simulation box

There is no box, so it can't move. There is a lattice specified by three lattice vectors defining the periodicity. These vectors are updated every step based on the pressure, if you use pressure coupling. You can specify the protein to have no net center of mass motion, by setting it as comm_grps i

Re: [gmx-users] Bootstrapping using g_wham

Hey, Most statistics texts on bootstrapping will advise taking in the order of a thousand bootstrap samples. Don't know about the number of bins, but in any case, the problem shouldn't be that hard computationally. Have you checked the process? Is it really still running, has it stalled? And how l

Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation [SOLVED]

On 6/15/12 6:53 AM, ms wrote: Ok, I am using v-rescale now and the major artefacts seem to be gone, at least on the very short term (2-3 ns). It seems grompp should warn that andersen is not a good choice if you're using CPUs :) Such a warning would become outdated very soon - the 4.6 devel

[gmx-users] Fwd: Regarding error.

-- Forwarded message -- From: Seera Suryanarayana Date: Fri, Jun 15, 2012 at 1:38 PM Subject: Regarding error. To: gmx-users@gromacs.org Dear all gromacs users, While i am running the commond "trjconv -f 1AKI_full.trr -s 1AKI_b4full.tpr -o final.

Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation [SOLVED]

Ok, I am using v-rescale now and the major artefacts seem to be gone, at least on the very short term (2-3 ns). It seems grompp should warn that andersen is not a good choice if you're using CPUs :) Thanks! M. -- Massimo Sandal, Ph.D. http://devicerandom.org -- gmx-users mailing listgmx-

Re: [gmx-users] Re: Positive Potential Energy after equilibration

On 6/15/12 4:08 AM, Satish Kamath wrote: Dear Users, I've managed to obtain a well equilibrated box of 2,3 dihydroxynaphthalene at 450K (melting point=437K) and 1 bar pressure. I've calculated hydrogen bond distance using g_hbond and it comes to 0.267 nm. I've also calculated the density and i

Re: [gmx-users] Bootstrapping using g_wham

On 6/14/12 5:51 PM, rainy908 wrote: Hi, I am currently using bootstrapping in g_wham to estimate the uncertainty in my PMF. I use a number of 1000 bootstraps. /software/gromacs/gromacs-4.0.7-plumed-1.2.0-x86_64/bin//g_wham \ -ip gwham.dat \ -bins 5000 \ -hist histo.xvg \ -bsres bsRe

Re: [gmx-users] help!!

On 6/15/12 5:58 AM, ankita oindrila wrote: i am using the tutorial KALP15 in DPPC for my protein in bilipid membrane SIMULATION. i have reached Step Three: Defining the Unit Cell & Adding Solvent where i hav to pack the lipids around the protein using InflateGro. how do i start using infl

Re: [gmx-users] Regarding error.

On 6/15/12 4:08 AM, Seera Suryanarayana wrote: Dear all gromacs users, While i am running the commond "trjconv -f 1AKI_full.trr -s 1AKI_b4full.tpr -o final.pdb -dump 500" i am getting the following warning. WARNING no output, last frame read at t=10 Kindly tel

[gmx-users] help!!

i am using the tutorial KALP15 in DPPC for my protein in bilipid membrane SIMULATION. i have reached Step Three: Defining the Unit Cell & Adding Solvent where i hav to pack the lipids around the protein using InflateGro. how do i start using inflategro? my last step was : to generate this new

Re: [gmx-users] protein near the edges of simulation box

Hi, All molecules diffuse. As such, proteins are expected to move about. Preventing them form doing so is essentially non physical, so you'd need a good and thought-through reason for doing so. Erik 15 jun 2012 kl. 10.27 skrev Shima Arasteh: > Thanks. > I read that it doesn't matter if the pr

Re: [gmx-users] protein near the edges of simulation box

On 15/06/2012 6:27 PM, Shima Arasteh wrote: Thanks. I read that it doesn't matter if the protein moves and even protrudes the box. It's OK, but there is a question here; why doesn't the box move rather than the protein? The box could move, but it can't accelerate, else it wouldn't be an http

Re: [gmx-users] current directory files

Thanks a lotnow it's working:) On Fri, Jun 15, 2012 at 2:00 PM, Mark Abraham wrote: > On 15/06/2012 6:21 PM, tarak karmakar wrote: > > Hi, > > Thanks for the reply. > One thing, while giving the '-ff' flag it is asking for some string. So I > renamed all my force field files as exc

Re: [gmx-users] current directory files

On 15/06/2012 6:21 PM, tarak karmakar wrote: Hi, Thanks for the reply. One thing, while giving the '-ff' flag it is asking for some string. So I renamed all my force field files as except spc.itp and ions.itp. Renamed files are . 1) ffprot.atp 2) ffprot.rtp 3) ffprot.itp [ includes ffn

Re: [gmx-users] protein near the edges of simulation box

Thanks. I read that it doesn't matter if the protein moves and even protrudes the box. It's OK, but there is a question here; why doesn't the box move rather than the protein? Is it possible for box to be defined every step?, then the protein would stay in the center of the box.   Sincerely,

Re: [gmx-users] current directory files

Hi, Thanks for the reply. One thing, while giving the '-ff' flag it is asking for some string. So I renamed all my force field files as except spc.itp and ions.itp. Renamed files are . 1) ffprot.atp 2) ffprot.rtp 3) ffprot.itp [ includes ffnonbonded.itp and ffbonded.itp ] pdb2gmx -f test.p

[gmx-users] Re: Positive Potential Energy after equilibration

Dear Users, I've managed to obtain a well equilibrated box of 2,3 dihydroxynaphthalene at 450K (melting point=437K) and 1 bar pressure. I've calculated hydrogen bond distance using g_hbond and it comes to 0.267 nm. I've also calculated the density and it comes to 1229 kg/m3 (solid density = 1120 k

[gmx-users] Regarding error.

Dear all gromacs users, While i am running the commond "trjconv -f 1AKI_full.trr -s 1AKI_b4full.tpr -o final.pdb -dump 500" i am getting the following warning. WARNING no output, last frame read at t=10 Kindly tell me how to overcome this error. Suryanarayana Seer

Re: [gmx-users] RE: Re: g_lie reproducibility

On 15/06/2012 8:30 AM, Tom Dupree wrote: Hi Mark, Thanks for the catch on the transcription error, I think I have found it ::embarrassed::. The repeated final value is still perplexing me. I have checked both my .xvg from g_energy and the .edr file with gmxdump. In both cases the final step (t

Re: [gmx-users] Re: Dihedral Constraints

Hi, This query is related to my previous queries. I want to constraint the psi/psi angle of the turn residue of my beta-hairpin , meaning that they are allowed to move in certain range of psi/phi angle space. Simultaneously, I want to freeze the movement of strand residues. This procedure has to

Re: [gmx-users] multi-chain pdbs with mdrun?

15 jun 2012 kl. 09.16 skrev Mark Abraham: > On 15/06/2012 5:06 PM, Samuel Flores wrote: >> >> HI Guys, >> >> I'm trying to run a short equilibration of p56 tetramer in water. I issue: >> >> /home/flores/local/gromacs/bin/mdrun -v -deffnm em -c >> /home/flores/projects/antibody-design/13JUN1

Re: [gmx-users] simulating dimer proteins

On 15/06/2012 3:56 PM, delara aghaie wrote: Dear Gromacs users I want to compare some properties of two Interferons via MD simulation. One comes with pdb ID : 1ITF. (It has 24 Models in single pdb file, but each model with single chain.) I did pdb2gmx on this. The other is with pdb ID of : (1R

Re: [gmx-users] analysing of the long trajectories

On 15/06/2012 3:50 PM, James Starlight wrote: Hi Tsjerk ! I my case I want to compare large-scale dynamics with more local events like fluctuation of the individual side chains so I suppose that I need larger number of frames. But how exactly I could define this number for my 100ns trajectory

Re: [gmx-users] Re: Preserving chain id/information when using editconf (gromacs 4.0.7)

hi Shay, Can you tell me how you resolved this? I'm having the same issue. Sam On Nov 1, 2010, at 12:10 PM, Shay Teaching wrote: > Sorry - problem resolved :-) > > On Mon, Nov 1, 2010 at 12:55 PM, Shay Teaching > wrote: > Hi everyone, > > I've come across some problem: I am simulating a pr

Re: [gmx-users] current directory files

On 15/06/2012 4:27 PM, tarak karmakar wrote: Dear All, In my protein pdb file I have changed some of the amino acid residue names. So accordingly I have changed corresponding residue names in force filed files and kept all the files [ modified and unmodified ] in my current working dir

Re: [gmx-users] multi-chain pdbs with mdrun?

On 15/06/2012 5:06 PM, Samuel Flores wrote: HI Guys, I'm trying to run a short equilibration of p56 tetramer in water. I issue: /home/flores/local/gromacs/bin/mdrun -v -deffnm em -c /home/flores/projects/antibody-design/13JUN12/352/last.2.em.pdb The problem is that last.2.em.pdb has four c

[gmx-users] multi-chain pdbs with mdrun?

HI Guys, I'm trying to run a short equilibration of p56 tetramer in water. I issue: /home/flores/local/gromacs/bin/mdrun -v -deffnm em -c /home/flores/projects/antibody-design/13JUN12/352/last.2.em.pdb The problem is that last.2.em.pdb has four chains, but none have chain ID's! The file I