[gmx-users] saving velocities and coordinates frequently

Hi , I wish to save velocities and coordinates every step for my system. For saving disk space i dont want to save water molecules. How can i do this ? Amit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http:/

Re: [gmx-users] Why does the -append option exist?

Well sometimes i run out of walltime when doing long simulations and append helps me not to do any file management after restarting simulations from the previous checkpoint. On Fri, Jun 3, 2011 at 3:26 PM, Dimitar Pachov wrote: > > At first, I thought the -append option of the mdrun command was

[gmx-users] local pressure calcuation for Gromacs-4.5

Dear all, I saw an unanswered post at http://lists.gromacs.org/pipermail/gmx-users/2011-January/058063.html It is about calculating local pressure in v 4.5 when using CHARMM FF. Could someone give me some pointers about this? Thank you Amit -- gmx-users mailing listgmx-users@gromacs.org ht

Re: [gmx-users] local pressure calcuation for Gromacs-4.5

Thanks Justin, I tried to install the recent git version but the configure file is missing. How should I install this version ? On Thu, Jun 9, 2011 at 12:45 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> Dear all, >> >> I saw an unanswered post

Re: [gmx-users] local pressure calcuation for Gromacs-4.5

119800.000 > ... > > Cheers, > Jianguo > > > > -- > *From:* Justin A. Lemkul > *To:* Discussion list for GROMACS users > > *Sent:* Friday, 10 June 2011 07:10:35 > *Subject:* Re: [gmx-users] local pressure calcuation for Gromac

[gmx-users] local pressure v4.5 issues

sly. Could someone help me in figuring our whats going on ? Amit Choubey -- 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)

[gmx-users] Re: local pressure v4.5 issues

in figuring out whats the issue ? Thank You. On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey wrote: > Dear all, > > I installed the git version of local pressure calculation from > > > http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure > > The I in

Re: [gmx-users] Re: local pressure v4.5 issues

s ? Could we compare our methodologies to use the local pressure version ? Amit > > Thank you very much! > > Cheers, > Jianguo > > > -- > *From:* Amit Choubey > *To:* Discussion list for GROMACS users > *Sent:* Monday, 20 June 2011

Re: [gmx-users] Re: local pressure v4.5 issues

me because i tried it over only two frames (3 reruns were done for two frames separately and a .trr which had these two frames only) and the numbers did not seem to be averages. Can someone help me in figuring out what is going on ? Amit On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey wrote: &

Re: [gmx-users] Re: local pressure v4.5 issues

and v4.0 from ? > Btw, did you use CHARMM FF in your simulations and how did you convert the > tpr files from v 4.5 to v 4.0? > Yes i have used CHARMM FF and i will have to figure out the conversion. > > Cheers > Jianguo > > -- > *From:* Amit

[gmx-users] gromacs 4.0 vs 4.5

Hi all, I am doing dppc-water simulation. I am using structure and topologies from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies In version 4.0 when i do grompp_v4.0.2 -v -c dppc128.pdb -o npt -f npt.mdp -p system.top it creates npt.tpr without any errors. Using the sam

Re: [gmx-users] gromacs 4.0 vs 4.5

Thanks Justin, I can see that there is no problem when i fix the periodicity. Amit On Tue, Jul 19, 2011 at 2:52 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> Hi all, >> >> I am doing dppc-water simulation. I am using structure and topologies from >

Re: [gmx-users] Re: local pressure v4.5 issues

of conversion tpr files from v4.5 to v4.0 using CHARMM FF? > > Thank you very much! > > Cheers, > Jianguo > > > > ------ > *From:* Amit Choubey > *To:* Jianguo Li > *Cc:* Discussion list for GROMACS users > *Sent:* Friday, 1 Jul

Re: [gmx-users] Re: local pressure v4.5 issues

ile to v4.0.2_local_pressure to rerun the simulation. > > Jianguo > > > -- > *From:* Amit Choubey > *To:* Jianguo Li > *Cc:* Discussion list for GROMACS users > *Sent:* Thursday, 28 July 2011 09:27:04 > > *Subject:* Re: [gmx-users] Re: local

[gmx-users] minor trjconv issue

Hi all, When i use the following trjconv_without_shock -f all_molecules_500ns_fixedpbc.gro -o traj.gro -novel -s npt.tpr traj.gro still has velocities. Amit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

Re: [gmx-users] minor trjconv issue

done On Thu, Jul 28, 2011 at 11:52 AM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> Hi all, >> >> When i use the following >> >> trjconv_without_shock -f all_molecules_500ns_fixedpbc.**gro -o traj.gro >> -novel -s npt.tpr >> &

Re: [gmx-users] Dimensionless units question

Hi, reduced units works for LJ particles only. I am not sure if it works when you include electrostatics. When you set charge = 1 it is 1electronic charge. I would suggest not to use the reduced units for LJ in this scenario. Amit On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall wrote: > Hi all,

Re: [gmx-users] Dimensionless units question

are their ratios, as there would still be a unit of length to > deal with. > > Thanks, > Alex > > On Fri, Jul 29, 2011 at 2:24 PM, Amit Choubey wrote: > >> Hi, >> >> reduced units works for LJ particles only. I am not sure if it works when >> you includ

Re: [gmx-users] Dimensionless units question

reference otherwise you cannot make the comparison. > > > I guess I'm not actually using gmx.ff, I was just using the C6-C12 > convention for LJ parameters used in that forcefield's ffnonbonded.itp. > > On Fri, Jul 29, 2011 at 3:50 PM, Amit Choubey wrote: > >&g

[gmx-users] how to simulate a line charge

Hi all, I am trying to do a calculation on an artificial line charge in vacuum. The line charge has 267 atoms and each atom has a 1e charge. The atoms are bonded by a bond term and an angle term. I defined the required itp files and top file. When i issue grompp_jpt -v -c parallel.gro -p chain.to

Re: [gmx-users] how to simulate a line charge

On Fri, Aug 12, 2011 at 8:55 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> Hi all, >> >> I am trying to do a calculation on an artificial line charge in vacuum. >> The line charge has 267 atoms and each atom has a 1e charge. The atoms are >&g

Re: [gmx-users] how to simulate a line charge

I change the maximum charge group size defined in the include/types/nblist.h header from 32 to 267. Then grompp worked fine but the mdrun did not start. The following error came out Program mdrun_jptlc, VERSION 4.5.3 Source code file: ns.c, line: 2417 Fatal error: Max #atoms in a charge group: 26

Re: [gmx-users] how to simulate a line charge

Thanks Bogdan, defining each atom as a charge group solves the grompp issue. Also here the atoms interact via non-bonded potentials. I think its a better way to simulate the line charge. Amit On Sat, Aug 13, 2011 at 8:29 AM, Bogdan Costescu wrote: > On Sat, Aug 13, 2011 at 05:43, Amit Chou

Re: [gmx-users] how to simulate a line charge

I was not sure if changing the size of maxcg would not negatively influence anything else. I will give it a try. Thanks Justin On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> I change the maximum charge group size defined in the >>

Re: [gmx-users] how to simulate a line charge

Justin, when i define the whole line charge as a charge group i do get a coulomb energy contribution. I thought there would be no non-bonded contribution. I use a very high cut-off (longer than chain length) and no pbc. Am i missing something ? On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey wrote

Re: [gmx-users] how to simulate a line charge

Sun, Aug 14, 2011 at 1:23 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> Justin, when i define the whole line charge as a charge group i do get a >> coulomb energy contribution. I thought there would be no non-bonded >> contribution. I use a very high cut

Re: [gmx-users] how to simulate a line charge

: > > > Amit Choubey wrote: > >> Following is the mdp file >> >> cpp = /usr/bin/cpp >> ;define = -DFLEX_SPC >> constraints = none >> integrator = steep >> nsteps = 1

Re: [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure

On Fri, Aug 19, 2011 at 8:50 AM, KONG Xian wrote: > I have sent this email days ago, but I got no answer. > > Hope someone would saw it this time. > > Sorry for disturbing. > > Dear all: > > I am using gromacs-4.0.2_localpressure to calculate the local > pressure of my s

Re: [gmx-users] use of the mailing list

On Fri, Aug 19, 2011 at 8:13 AM, Junior Nebeker wrote: > Sure Mark. If your interest is in patrolling the Gromacs mailing list, > then I'll leave you to it. > I think before you type your response you should consider that Mark has helped several hundred times over this mailing list. > On Thu,

Re: [gmx-users] distance between mass center of two groups

Use g_dist tool. On Sun, Aug 28, 2011 at 8:38 AM, Sajad Ahrari wrote: > Dear users, > is there any command in Gromacs to show fluctuations of distance, between > mass center for two groups of amino-acids in a protein, over time? > thanks, > sajad > > -- > gmx-users mailing listgmx-users@gro

Re: [gmx-users] 3D pressure profile of a bilayer

On Tue, Sep 6, 2011 at 10:07 PM, Shou-Chuang Yang wrote: > Dear gmx-users, > > Could anyone help me with the calculation of 3D pressure profile in a > function of y? > I used the provided gromacs-4.0.2_localpressure for my calculatioin. It > calculate > the 3D pressure profile as a function of z (

Re: [gmx-users] 3D pressure profile of a bilayer

On Wed, Sep 7, 2011 at 12:30 AM, Shou-Chuang Yang wrote: > > > On Wed, Sep 7, 2011 at 12:11 AM, Amit Choubey wrote: > >> >> >> On Tue, Sep 6, 2011 at 10:07 PM, Shou-Chuang Yang wrote: >> >>> Dear gmx-users, >>> >>> Could

[gmx-users] Using CHARMM 36 for DPPC simulation

5Hello all, I am trying to use CHARMM 36 for DPPC membrane simulation. I did the following so far: 1. Download pdb file containing 128 DPPC molecules from http://www.charmm-gui.org/?doc=archive&lib=lipid_pure 2. I separated one lipid molecule from the obtained pdb file and used pdb2gmx -f 1dppc.

[gmx-users] Re: Using CHARMM 36 for DPPC simulation

Hi Everyone, I did another simulation where i found the the DPPC area per lipid is 0.61 nm^2 . Is this acceptable ? I have seen issues like this on the mailing list before can one of the experts give me some hints. Amit On Wed, Nov 9, 2011 at 12:24 PM, Amit Choubey wrote: > > 5Hel

[gmx-users] hi questions about installing GROMACS

hi, I am trying to install GROMACS (version 4.0) on my local machine. I tried to follow the supplied simple instruction in the INSTALL file. The ./configure step works but the "make" command doesnt work. My bash prints out "make: *** No targets specified and no makefile found. Stop." What should

Re: [gmx-users] Re: hi questions about installing GROMACS

hi, thank you for extending the help but luckily i have figured out what was going wrong. I have been able to install the package. Thank you, Amit On Fri, Sep 4, 2009 at 1:30 PM, Vitaly V. Chaban wrote: > I am trying to install GROMACS (version 4.0) on my local machine. I tried >> to >> follow

[gmx-users] how to use a new force field

hi gromacs user, Is there any good way to introduce new force field in the gromacs library? Amit ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/s

Re: [gmx-users] how to use a new force field

Hi, so is it a good idea to edit the original gromacs files in top directory for introducing new force field or is there a way to compliment the existing FF files by a new file made by me? Amit On Tue, Sep 8, 2009 at 2:38 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > &

Re: [gmx-users] how to use a new force field

make pdb2gmx aware of the new FF files. Amit On Tue, Sep 8, 2009 at 6:58 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> Hi, >> >> so is it a good idea to edit the original gromacs files in top directory >> for introducing new force field or is ther

Re: [gmx-users] how to use a new force field

By the way thank you very much for answering my questions. Amit On Tue, Sep 8, 2009 at 7:13 PM, Amit Choubey wrote: > hi, > ok the next question that bugs me is if i make a directory consisting of my > modified force field (*.atp, *.rtp, *bon.itp,*nb.itp) and i want to use > pdb2gm

Re: [gmx-users] how to use a new force field

l Parade, Parkville VIC 3010 > dallas.war...@pharm.monash.edu.au > +61 3 9903 9167 > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf

[gmx-users] bypassing pdb2gmx

hi everyone, I have a pdb file of my system and i want it to be fed into the GROMACS software. I have a new force field for the simulation and i have made the .top file manually which includes the new library FF files. I need to get a .gro file from the .pdb file that i have. So, is there a way out

[gmx-users] pdb2gmx question

hi everyone, I am trying to set up a very small simulation with DPPC lipid. I am using the GROMOS96 53a6 FF. Now i have my pdb file which looks like ATOM 1 C33 DPPC1 15.771 52.651 9.201 1.00 0.00 ATOM 2 C34 DPPC1 16.750 52.953 11.353 1.00 0.00 ATOM 3

[gmx-users] Re: bypassing pdb2gmx

On Wed, Sep 9, 2009 at 5:29 PM, Amit Choubey wrote: > hi everyone, > I have a pdb file of my system and i want it to be fed into the GROMACS > software. I have a new force field for the simulation and i have made the > .top file manually which includes the new library FF files. I n

Re: [gmx-users] Re: bypassing pdb2gmx

thanks a bunch for the input. On Thu, Sep 10, 2009 at 9:38 AM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> hi everyone, >> >> I guess if i knew the exact format of .gro files i could write a small >> code to copy data from pdb to gro . I cannot f

[gmx-users] mpi version of gromacs

Hi everyone, I have the gromacs mpi version on my system and everything in the simulation works fine until i get to mdrun_mpi and when i use this executable the following pops error comes up MX:hpc-login2:mx_init:querying driver:error 5(errno=2):No MX device entry in /dev. Then i tried the to do

Re: [gmx-users] mpi version of gromacs

command line wrong? On Tue, Sep 15, 2009 at 6:25 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> Hi everyone, >> >> I have the gromacs mpi version on my system and everything in the >> simulation works fine until i get to mdrun_mpi and when i use t

[gmx-users] analyzing gromacs trajectories on VMD

hi everyone, I want to analyze the gromacs trajectories using vmd, is there a quick way of doing so ? Is there a reference for this? Thank you Amit ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Pl

[gmx-users] question about chain identifier

hi everyone, I had a question about the purpose of chain identifier character in pdb. What does it mean for Gromacs, i mean what does gromacs do with it? I actually have a "bad" pdb file which has *different* chain identifiers for first few molecules of the same type and then there exists none for

[gmx-users] using 'genbox' for adding solvent

Hi everyone, I have been trying to insert a fixed no. of water molecules in my system. I first tried the -cp -cs options and could insert some water molecules. But I still need to insert few more water molecules and for that i tried using the -nmol -ci option. I made a file named "insert.gro" whic

Re: [gmx-users] using 'genbox' for adding solvent

Sun, Sep 20, 2009 at 6:38 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> Hi everyone, >> >> I have been trying to insert a fixed no. of water molecules in my system. >> I first tried the -cp -cs options and could insert some water molecules. B

Re: [gmx-users] using 'genbox' for adding solvent

yes you are right its a bug, everything works well on the most recent version. Thank you On Sun, Sep 20, 2009 at 6:55 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> I still want to suggest that segmentation fault doesn't occur due to large >> no. of i

[gmx-users] question about energy minimization

box dimensions as I started with. Could someone help me in understanding what happened? Thank you, Amit Choubey ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Re: [gmx-users] question about energy minimization

Hi Omer, My question was to how to avoid the "diffusion" of molecules out of the box during energy minimization and MD run? I think what you suggested here will just change the present trajectory into a new by using the pbc condition. But i am wondering shouldnt this be done in MD calculation it

[gmx-users] defining a 3 body user defined potential

Hi all, I was wondering if there is a way to define user defined potential which involves 3 particles. Thank you for any input. Amit -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Suppor

Re: [gmx-users] defining a 3 body user defined potential

t impossible and it was already done > for TIP4P, see Kumar and Skinner, J. Phys. Chem. B, 112,8311-8318, 2008 > > I hope this help > Ivan > > Amit Choubey wrote: > > Hi all, > > > > I was wondering if there is a way to define user defined potential which &

Re: [gmx-users] request

Hi, Define an itp file which has the non-bonded info. Then define a mdp (md parameter file) and also make a structure file (gro). Also you need a topology file (top) which corresponds to the structure file. You will have to do some background work. Manual should be your friend. amit On Sat, Nov

[gmx-users] question on KALP-15 in DPPC tutorial

Hi all, I was going through the very nicely presented tutorial by Justin (on KALP-15 in DPPC). I have one question regarding the non-bonded cut-offs. It seems that people use many different values of non-bonded cut-off (varying from 0.9 nm to 1.2 nm or probably more). How should i choose the cut-o

Re: [gmx-users] question on KALP-15 in DPPC tutorial

Thank you Mark and Justin. Yes i did check the reference of your tutorial, but its just that there are so many groups using same FF but different cut-off lengths. amit On Sun, Nov 21, 2010 at 10:22 AM, Justin A. Lemkul wrote: > Quoting Mark Abraham : > > > On 21/11/2010 8:45 PM,

[gmx-users] dna, lipid simulation

Hi all, This is a question unrelated to gromacs but would pose it anyway to get some hints from the experts. I wish to set up DNA and DPPC lipid membrane simulation. Could someone please refer to a relevant forcefield/tutorial for simulation of lipids with DNA? Any help will be really appreciated

Re: [gmx-users] dna, lipid simulation

parameters by > David Poger and Alan Mark which I should give better results compared to the > old set. > > Good luck. > > > On 5 December 2010 18:09, Amit Choubey wrote: > >> Hi all, >> >> This is a question unrelated to gromacs but would pose it anyway t

Re: [gmx-users] Hard Spheres

On Wed, Dec 8, 2010 at 4:01 AM, Sascha Hempel < sascha.hem...@bci.tu-dortmund.de> wrote: > Hi all! > > I am trying to add some hard spheres to my simulation. As far as i can > tell from the manual Gromacs supports only LJ or Buckingham for > non-bonded interaction. > Why cant you use LJ? By sett

Re: [gmx-users] -symm option

try using to find out, its described on http://manual.gromacs.org/current/online/g_density.html On Wed, Dec 8, 2010 at 4:10 AM, Morteza Khabiri wrote: > Dear all > > does somebody knows how -symm option from g_density command do the > calculations? > Or in other word what is the basic of -symm op

Re: [gmx-users] CMAP error

This may not be related but it was not straight forward to do DPPC membrane simulation using CHARMM FF in gromacs. The DPPC molecule was not defined at all in the FF files. The DPPC is defined in terms of two more residues in CHARMM. amit On Thu, Dec 9, 2010 at 11:21 AM, Justin A. Lemkul wrote:

Re: [gmx-users] box size & continuing the previous energy minimization

On Thu, Dec 23, 2010 at 2:41 PM, mustafa bilsel wrote: > Hi, > > 1. How can I learn the box shape and size of a completed simulation? > check the end of the resulting gro file . > 2. I want to keep going the previous completed energy minimization by > increasing nsteps. How can I do this? > i

Re: [gmx-users] Signal: Segmentation faul

Your log file does indicate that the steepest descent converged. I dont know why you have the error messages. Why not go ahead with MD ? Amit On Sun, Jan 2, 2011 at 10:35 PM, shikha agarwal wrote: > hi, > HAPPY NEW YEAR > > I am experiencing a segmentation fault during mdrun in equlibration step

Re: [gmx-users] so difficult problem

There is something wrong with your initial configuration. May be you forgot to take care of periodicity, how did you get your initial configuration? Also notice that these kind of problems have been discussed previously. Amit On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour < ramezanpour.moh..

Re: [gmx-users] so difficult problem

te them. > I could pass all of steps in UMbrella sampling tutorial with these > files,without any warning or error. > the one thing I changed is rotating box with editconf. > > > > > On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey wrote: > >> There is something wron

Re: [gmx-users] so difficult problem

; Thanks in advance > > > On Tue, Jan 4, 2011 at 12:56 PM, Amit Choubey wrote: > >> May be you broke the molecule while using editconf. Try to fix the >> periodicity by trjconv and then use it. >> >> >> On Tue, Jan 4, 2011 at 1:14 AM, mohsen ramezanpour <

Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

try the -type option with dihedral amit On Fri, Jan 7, 2011 at 2:16 AM, Carla Jamous wrote: > Hi Everyone, > > Please I'm trying to calculate one dihedral angle as a function of time > during my simulation. > For this, I used g_angle. In the manual (version 4.0.3) it says: the > indexfile shoul

Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

ngle of a group of angles as a function of time!! > What does it mean? > > Because I'm getting positive and negative values in the same plot. Are > these values the values of my dihedral angle as a function of time? > > Thanks again, > Carla > > > On Fri, Jan 7, 2

Re: [gmx-users] trjconv with multiple chains

Make your box bigger? 2011/1/6 yuanyuan wang > dear all, > I am doing a simulation that have many chains in a box , and I can > find a center for them after serval tries. > I use almost every option of trjconv,-pbc > mol,atom,res,whole,nojump , -ur compact, -center , -box to go

Re: [gmx-users] Energy minimization

Can you provide more details ? Which graph are you talking about ? Amit On Mon, Jan 17, 2011 at 12:05 AM, bharat gupta wrote: > Hi all, > > I am minimizing my protein (230 amino acids) with the minim.mdp file given > in the lysozyme tutorial but I am not getting a stable graph .. I checked > th

Re: [gmx-users] Energy minimization

OK what seemed wrong to you? On Mon, Jan 17, 2011 at 12:24 AM, bharat gupta wrote: > I am doin the first minimization step.. here are the details of minim.mdp > file > > ; minim.mdp - used as input into grompp to generate em.tpr > ; Parameters describing what to do, when to stop and what to save

Re: [gmx-users] Energy minimization

Check your log file to see if the minimization criterion was satisfied ie the max force is less than emtol. On Mon, Jan 17, 2011 at 12:29 AM, bharat gupta wrote: > > The potential energy graph is not coming parallel to x-axis is getting down > towars the x-axis .. normally it should be paralle to

[gmx-users] spurious forces while doing pulling simulation

Hi all, I am trying to do pulling simulation. Following are the pull parameters pull = umbrella pull_geometry = direction pull_vec1 = 0 0 1 pull_group1 = RNA pull_rate1 = 0.01 pull_k1 = 1000 pull_start = yes Everything works fine until the pull group COM reaches half the box length. The COM posi

Re: [gmx-users] spurious forces while doing pulling simulation

. Lemkul wrote: > > > Amit Choubey wrote: > >> Hi all, >> >> I am trying to do pulling simulation. Following are the pull parameters >> >> pull = umbrella >> pull_geometry = direction >> pull_vec1 = 0 0 1 >> pull_group1 = RN

Re: [gmx-users] spurious forces while doing pulling simulation

Hi, I am still not able to see the reason for the periodic distances coming into picture. Also, why pull_geometry = direction_periodic cannot be used with P-coupling; although it seems to do what i want. Amit On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey wrote: > Hi, > > Initially,

Re: [gmx-users] spurious forces while doing pulling simulation

(using pull_init1) should fix this issue but i am not confident. Thanks for looking into this. On Mon, Jan 17, 2011 at 5:36 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> Hi, >> I am still not able to see the reason for the periodic distances coming >> i

Re: [gmx-users] spurious forces while doing pulling simulation

It seems that i cannot figure out a way to change the absolute reference point (Its the origin by default). Amit On Mon, Jan 17, 2011 at 5:52 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> Yes Justin i understand that. Heres what i think is going on >> >

Re: [gmx-users] Problem: Protein move out of box

you can use trjconv -pbc nojump to take care of that. On 10/8/09, Pan Wu wrote: > Hi Gromacs users,I am new to Gromacs, and now setting up one very simple > system to test Gromacs+Martini. (one protein with solvent surrounded) > When I run the MD and saw the trajectory, the protein seem

[gmx-users] increasing the system size

Hi everyone, I was looking for ways to increase the system size (no. of atoms) beyond 9 . I read somewhere that there is no inherent constraint in gromacs on system size rather its because of the format of .gro . I cant find where i read this but could someone suggest me what to do if i need t

[gmx-users] creating a larger lipid membrane

Dear Gromacs Users, I have been trying to generate a larger lipid system but am running into troubles due to improper initial co-ordinates set up. Following are the steps i am trying to follow. 1. I start with a 128 dppc membrane and use genconf to create a larger system. I got the dppc128.pdb fro

Re: [gmx-users] creating a larger lipid membrane

Hi Justin, Yes you are right. I didnt fix the periodicity to start with. Could you tell me how to do that, which command to work with? Thanks. amit On Fri, Oct 9, 2009 at 5:39 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> Dear Gromacs Users, >> >> I

Re: [gmx-users] creating a larger lipid membrane

, 2009 at 5:44 PM, Mark Abraham wrote: > Amit Choubey wrote: > >> Dear Gromacs Users, >> >> I have been trying to generate a larger lipid system but am running into >> troubles due to improper initial co-ordinates set up. Following are the >> steps i am trying to

Re: [gmx-users] creating a larger lipid membrane

Thank you for the tip. I will try to use it. Amit On Fri, Oct 9, 2009 at 6:10 PM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> Hi Justin, >> >> Yes you are right. I didnt fix the periodicity to start with. Could you >> tell me how to do that, w

Re: [gmx-users] trr file in VMD

yes you can do that by opening the gro file and then loading the .trr file . amit On Sun, Oct 11, 2009 at 6:22 PM, Paymon Pirzadeh wrote: > Hello, > How can we use the trr file in VMD? I thought since we ask in the mdp > file to output the velocities, then in VMD we should be able to see > molec

[gmx-users] question about all atoms lipid molecule structure and force field

Dear all, I have been trying to search for an all atom DPPC sructure (including the missing Hydrogens of long chain hydrocarbons) and then do an all atoms md simulation on it. I havent yet found any such structure or any force field that could be used for it on the internet. Is anybody familiar wit

Re: [gmx-users] question about all atoms lipid molecule structure and force field

Thank you, Is it really necessary for me to use Charmm FF for all atom calculations on lipids? The reason I am asking this is because it will require me to create gromacs compatible FF files of the Charmm FF . I did find two perl scripts which can do probably handle that but i am wondering if the

Re: [gmx-users] question about all atoms lipid molecule

Hi Par Bjelkmar, I need to do an all atom simulation for dppc bilayer . You are right the dppc molecule file that i have has PALM and PCGL residues. I will like to try to set up the charmm FF for gromacs. But I dont have the FF files with me, neither do i have the programs. Could you send me a tu

[gmx-users] gromacs wall parameters

Hi everyone, I am trying to model an impenetrable wall for my simulation at z=0. I read the manual where this thing is discussed. I am still doubtful about the options to use. It seems that the wall parameters are designed to figure out the repulsive potential function based on wall_type, wall_at

[gmx-users] Setting up an infinitely hard wall

Hi everyone, I have been trying to set up an "infinitely" hard potential wall. I tried to use the available wall options and could not really get it to do what i needed. I wanted a steep repulsive potential but when i created that, the system was blowing up, reason being that it requires smaller t

Re: [gmx-users] POPG-Martini Force Field

On Thu, Oct 22, 2009 at 9:53 AM, S hv wrote: > Hi, > > I am currently working with peptide/lipids interactions using the martini > force field. I want to built a bacterial membrane, so I trying to find the > topology of the POPG lipid but until now without success. > > > In the martini_v2.0_li

[gmx-users] Setting up an infinitely hard wall

Hi everyone, I am sending this email again hoping for any quick input for my question. I have been trying to set up an "infinitely" hard potential wall. I tried to use the available wall options and could not really get it to do what i needed. I wanted a steep repulsive potential but when i cr

Re: [gmx-users] Setting up an infinitely hard wall

Hi Berk, Thank you for the response. I have obtained distributions with in infinite wall by simulating with an > softer wall > and unbiasing with configurations with the wall potential. > Could you explain the above ? I am not sure if i get your point. > But if you need the dynamics, or you wan

Re: [gmx-users] POPG-Martini Force Field

On Fri, Oct 23, 2009 at 12:33 AM, XAvier Periole wrote: > > On Oct 22, 2009, at 11:28 PM, Amit Choubey wrote: > > > > On Thu, Oct 22, 2009 at 9:53 AM, S hv wrote: > >> Hi, >> >> I am currently working with peptide/lipids interactions using the ma

Re: [gmx-users] Setting up an infinitely hard wall

Hi Berk, I am mailing about the issue of setting up infinite potential well. I now want to simplify the task of inversing the velocity and mirroring the particle by the following procedure. If a particle is found in z wrote: > Hi, > > If you have a wall potential, you can reweight the configura

[gmx-users] calculating local pressure

Hi Everyone, I have been looking at ways to calculate local pressure for a simulation. I found a gromacs package called gromacs-localp-3.0.2.tgz at the following page http://www.gromacs.org/index.php?title=Download_%26_Instal

[gmx-users] Re: Walls In Gromacs

On Tue, Nov 10, 2009 at 4:32 AM, Marcovitz Amir wrote: > Hi Amit, > > Unfortunately, i don't have an answer to your question as i am a very > new GROMACS user myself.. > Actually i might need your help. > > I need to model two charged plates with opposite signs which are > solvated in an electro

[gmx-users] doing exact continuation

Hi everyone, I want to do an exact continuation with saved configuration and velocity. What are the options that i need to change in mdp file? I know i have to make unconstrained_start = yes. Anything else? The reason i am asking this is that it is kind of difficult to make sure if i am doing th

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