[gmx-users] trjconv in Parallel run

Hi all, I have been running mdrun in Parallel for few hours due to full disk it crashed in between, later when I use trjconv command trjconv -f .trr -o xtc for convert .trr to .xtc its showing "Program trjconv, VERSION 3.3.1 Source code file: trnio.c, line: 66 File input/output error: Can not det

[gmx-users] Energy minimisation

Hi gmx-users, I am having small doubt on energy minimisation that is I have started protein system, when I do EM its showing that Step size too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 800 Double precision normally gives you higher a

[gmx-users] Re: Protein coming out of the box

Oh...Similar type of problem once I have got, so got reply from some one in archives that if use comm_grps= protein , protein will not come out of the water box.So thats why I have suggested, If I say wrong answer regret for that >* Hi, *>* Ravi *>* Use comm_grps = protein in your .mdp file. *>

[gmx-users] Re:Protein coming out of the box

Hi, Ravi Use comm_grps = protein in your .mdp file. > > 3. protein coming out of the box (ravi sharma) > > > Hello everyone > > my protein coming out of the box in final md how can i fix my protein in > the middle of the box. can you help me out?? > > > ___

[gmx-users] Re: gmx-users Digest, Vol 54, Issue 15

Thanks Justin for the response and clear explanation about water models. This link ( http://en.wikipedia.org/wiki/Water_model ) tells that SPC water model has 109.47 degree, so TIP3P angle is relevant to physiological solvent. In AMBER also mostly TIP3P water model is using rather than SPC. I am u

[gmx-users] tip3p water model

Hi gmx-users, I want to use tip3p water model when I mention this model with flag -cs by genbox command it showed that no program for tip3p.gro, from this link http://www.gromacs.org/pipermail/gmx-users/2007-February/025712.html I understood that mention -spc water model in genbox command but in .t

[gmx-users] Re:Error in T-coupling of 2 atoms in T-couplingGroups

> > Hi Chitrita, may be you haven't generated index file for the solvent and newly added ions > use make_ndx file > all the best Sudheer. > > I am a beginner of Gromacs 3.3.3. > > I have done position restrined grompp with -f pr.mdp, -r .gro (water box > having

[gmx-users] different versions of Gromacs

Hi Users, I want to compare the protein results by simulating six systems in personal computer has Gromacs version 3.3.1, due to delay of running jobs in a single computer,I want to run some of my systems in another computer contain Gromacs version 3.3.3 but processor speed machine type everything

[gmx-users] Unequal water of Bilayer system in *PR step

> > Thank you very much to Xavier for your valuable suggestion > >>> > Hi Users, > >> >> > I have extended the lipid bilayer(popc) from default > >> >> popc128a.pdb to > >> >> > 200 popc molecules with suffcient water by using genbox. > >> >> > genbox -cs 128a.pdb -o o

[gmx-users] Re: Unequal water of Bilayer system in *PR step

>> > Hi Users, > >> > I have extended the lipid bilayer(popc) from default > >> popc128a.pdb to > >> > 200 popc molecules with suffcient water by using genbox. > >> > genbox -cs 128a.pdb -o out.gro -p 128a.top -box 9.2 9.2 6.9, > >> to the > >> > out.gro(co

[gmx-users] Re:Unequal water of Bilayer system in *PR step

- > > > > > Hi Users, > > I have extended the lipid bilayer(popc) from default popc128a.pdb to > > 200 popc molecules with suffcient water by using genbox. > > genbox -cs 128a.pdb -o out.gro -p 128a.top -box 9.2 9.2 6.9, to the > > out.gro(contain 200 popc) minimisation ran fine later swti

[gmx-users] Unequal water of Bilayer system in *PR step

Hi Users, I have extended the lipid bilayer(popc) from default popc128a.pdb to 200 popc molecules with suffcient water by using genbox. genbox -cs 128a.pdb -o out.gro -p 128a.top -box 9.2 9.2 6.9, to the out.gro(contain 200 popc) minimisation ran fine later swtich over to *PR with fc-100

[gmx-users] tpbconv*

Hi users, I am running membrane protein simulation in between system crashed due to power fluctuations, I am trying to extend this run by using tpbconv command tpbconv -f 1ns.trr -e 1ns.edr -s 1ns.tpr -o new1ns.tpr it showed that Reading toplogy and shit from 1ns_2timeTh6_9inpopc.tpr Reading file

[gmx-users] lipidposre.itp file of popc

Hi gmx-archives, I want do *PR for popc with restrain specifically on P(8),C(50),CA1(50) of all popc molecules, I wrote lipidposre.itp file like this [ position_restraints ] ; atom type fx fy fz 8 1 500 500 500 501 500 500 500 511 500 500

[gmx-users] Re: gmx-users Digest, Vol 53, Issue 81

if you simulate a > smaller protein, less lipids may be sufficient. You may also want to use > a hexagonal box which will allow you have less lipids and water. > > cheers, jochen > > sudheer babu wrote: > > Hi gmx-users, > > whats the number of POPC molecules shou

[gmx-users] POPC number

Hi gmx-users, whats the number of POPC molecules should be there after inserting protein into popc? In my case 90 popc molecules are there around the protein from 128 molecues which I downloaded from Dr.Tielman's website. Any suggestion will be appreciated Thanks in advance. __

[gmx-users] Understanding about grompp and tpbconv

Hi gmx-users, I have doubt about grompp and tpbconv commands. I am telling like this If I run grompp each time with interval of 1ns until 10ns md simulations, considered as one system. By using tpbconv eachtime with same interval time 1ns unitl 10ns simulation considered as a another system. Both o

[gmx-users] Re: gmx-users Digest, Vol 53, Issue 23

installtion commands usual goodluck sudheer. Dear gmx users, > > fftw3 seems doesn't support MPI. > Why is the gromacs configuration default fftw3 not fftw2? > Which version should I use for parallel computing? > > Thank you. > > >

[gmx-users] Re:

Thank you Justin. > sudheer babu wrote: > > Hi all, > > I want to ask two questions > > 1.I am interested to calculate electron density of -CH3 group of popc > > bilayer, Is it require to consider (CH3)3 surround by N and CH3 at > > tails also or consider CH

[gmx-users] CH3 group and units of POPC?

Hi all, I want to ask two questions 1.I am interested to calculate electron density of -CH3 group of popc bilayer, Is it require to consider (CH3)3 surround by N and CH3 at tails also or consider CH3 at tails only? 2. I have calculated electron density of PO4, water, N(CH3)3 groups of popc, groma

[gmx-users] Re: gmx-users Digest, Vol 51, Issue 102

e the way iam doing whether correct or not? this may be trivial question but i am new to gromacs. any suggestion would be appreciated. > > > sudheer babu wrote: > > Hi, > > I would like to calculate B-factor of protein, so I performed > > command like this > >

[gmx-users] g_rmsf

Hi, I would like to calculate B-factor of protein, so I performed command like this g_rmsf -f .xtc -s .tpr -res -o fluctuate.xvg -od devi.xvg it has run without error.Now i am bit doubting that which .xvg file have to take for plot B-factor values? B-factor is nothing but thermal devat

[gmx-users] Which ensemble for membrane proteins?

Hi everybody, I have read one review article( dissertations.ub.rug.nl/FILES/faculties/science/1998/d.p.tieleman/c1.pdf ) about membrane proteins tells about POPC alone simulations should run in NPT but not in NVT conditions. Regarding protein run in both some time NPT remain time

[gmx-users] High number of steps are adding

Hi , When I run tpbconv command for extending run its adding high number of steps rather than I need, The command line is *tpbconv -f .trr -s .tpr -e .edr -o out.tpr -extend 1000 it has run without error at final lines it showed that Extending remaining runtime of by 1000 ps (now 550 st

[gmx-users] how to select 'P' atom for g_msd

Hi Users, I want to calculate lateral diffusion coefficent of popc bilayer by using g_msd , the information I understood from one journal ( http://dx.doi.org/10.1063/1.2393240) is that P atom select and feed to g_msd command . I have to take only single P atom or all Patoms of POPC b

[gmx-users] Re:: Specified frame doesn't exist or file not seekable

.xtc format, so I am trying to get 7ns file in .trr format for continue my simualation Thanks in advance. sudheer babu wrote: >* Hi all, *>*I am having 7.25ns trajectory file , I am trying to pick up *>* 6250ps to 7250 ps trajectory file from whole trajectory by usin

[gmx-users] Specified frame doesn't exist or file not seekable

Hi all, I am having 7.25ns trajectory file , I am trying to pick up 6250ps to 7250 ps trajectory file from whole trajectory by using trjconv, Command line is *trjconv -f 7.25ns.xtc -s pr.tpr -o 6.25_7.25_out.trr -b 6250 -e 7250 selected " system " for getting output it s

[gmx-users] Re:confusion regarding tpbconv

shall we mention in this way? steps: 1- tpbconv -f old.trr -e old.edr -s old.tpr -o new.tpr 2- mdrun -v -deffnm new.tpr Thanks in advance. On Mon, 12 May 2008 15:10:32 +0530 "Anamika Awasthi" <[EMAIL PROTECTED]> wrote: > Dear Friends, >If my simulation crashed because of power failure,

[gmx-users] Re:restart run problem

Thanks for reply Justin, I have given run 375000 steps but in between simulation stopped, in terminal showed that segmentation fault and in .log file showed that "t = 650.000 ps: Water molecule starting at atom 14549 can not be settled. Check for bad contacts and/or reduce the time step.Wrote pdb f

[gmx-users] restart run problem

HI all, My simulation crashed mid of the run , I genrated restart.tpr by using tpbconv command for restart my simulation, Then I when I give mdrun -v -deffnm restart.tpr It showed below mentioned two lines and stopped. "Wrote pdb files with previous and current coordinates step 0, will finish at

[gmx-users] Running simulations in different versions

HI all, I have run 3ns lipid simulaiton by using gromacs 3.3 version and protein in 3.3.1 version. Now I want to run 3ns lipid with protein(both) in 3.3.1 version, will it cause any effect during anlaysis. Thanks for your appreciation. ___ gmx-users mail

[gmx-users] Fatalerror: Couldnt write energies

Thanks David for reply. No,.edr which crahsed contain 216kb. sudheer babu wrote: >* Thanks Mark for your reply, My system is neither full nor didnt do *>* anything with .edr file, I did same simulation again, same problem I got *>* that stopped my simulation and showed "fatal er

[gmx-users] Fatal error:couldn't write energies

Thanks David for your reply . No, the crashed .edr has only 216kb. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don'

[gmx-users] Re: Fatal error:couldnt write energies

Thanks Mark for your reply, My system is neither full nor didnt do anything with .edr file, I did same simulation again, same problem I got that stopped my simulation and showed "fatal error: could not write energies" Pls suggest me. Thanks in advance sudheer babu wrote: >* HI gmx-u

[gmx-users] Fatal error: Could not write energies

HI gmx-users, Iam simulating POPC lipids in water,I have done minimisation,equilibration and production, Till 2ns ran fine but when iam trying to run 2.5 ns run mid of the simulation at 18650 step it crashed and showed error Pls suggest me my md.mdp file is title = popc_prod const

[gmx-users] How to modify H atom type from opls_369 to match H expected by popc.itp

Hi all, Two days back I posted this question, no one replied thats why I am posting again. I wanted to use OPLS-AA/L force field for POPC and Protein 1.I calculated the sigma and epsilon values as the way Mr.Justin mentioned , the values I got are ;name name charge mass charge ptype

[gmx-users] modify H atom type from opls_369

tin has mentioned. >Sudheer, please note that the original post that you quote below actually includes an example for LO LO > "LO LO 115.9994 0.000 A2.96000e-01 8.87864e-01" >Also note that similar information is available in that post for pairtypes.

[gmx-users] H Atom type modification of POPC and double pair

Hi all, Thanks for the response to Mr.Justin and Mr.Chris I calculated the sigma and epsilon values in the way Justin mentioned the values are ;namename charge mass charge ptypesigma epsilon LO LO 115.9994 0.000 A0.29514 0.878694594

[gmx-users] OPLS-AA/L

Hi all , I wanted to use OPLS-FF for POPC and Protein, I followed the procedure from archives and the link is *http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html* The steps I have done are 1. I added "atom types" from lipid.itp to ffoplsaanb.itp here I got no exponential values

[gmx-users] OPLS-AA/L

Hi all, I am using gromacs 3.3.1 version.How can I generate OPLS-AA/L FF for POPC Thanks in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/

[gmx-users] OPLS-FF

Hi all, My protein contain some missing residues , so I rebuilt missing residues, although gap is there between helices, my idea is when do minimisation these gap should disappear. Later trying to use pdb2gmx with OPLS/aa-L FF for generating gro file for two systems containing protonated and anothe

[gmx-users] FF for membrane protein simulation in water

Hi all, I want to simulate my protein in water first, later insert into POPC bilayer. Could you suggest which force field use protein in water and protein in POPC, it should be same or different FF in both cases. Pls help me.. Thanks in advance. ___ gmx-u

[gmx-users] problem about rmsd

Thanks for your reply, I am mentioning commands, from crashing the simulation 1. tpbconv -f protein.trr -s protein.tpr -e protein.edr -n index.ndx -o out.tpr 2.mdrun -v -deffnm -o out.tpr 3.trjcat -f 633ps_pro.xtc 1ns_pro.xtc -settime -o it asked time I mentioned 0 and 633, then it shown that

[gmx-users] problem about rmsd

Hi all, I gave 1ns run production step without velocities in md.mdp file, in between my simulation crashed, so I used *tpbconv for continue that crashed run , After finishing that I used *trjcat for catenation of my 2 simulation trajectory files, its shown only 900ps trajectory files into trjout.xt

[gmx-users] Problem about tpbconv

Hi all, I am runnning system with 1ns NVT production step without velocities in md.mdp file, inbetween the simulation was crashed because power problem and I want continue the run from where it was stopped by using *tpbconv but it shown warning, fatal error and finally stopped without generating ou

[gmx-users] problem of FF

Thanks for your reply, Shall I use FF in this way that first protein in water simulaiton use "GROMOS96 43a1 FF" incase of only protein, after inserting protein into POPC bilayer, the GROMOS96 43a1 wont recognise because mixed FF , So can I use ffgmx for protein incase of both systems by using pdb2

[gmx-users] Problem about *FF

Thank you very much Mr.Andreas for reply, As I told you, used deprecated FF for protein, after insertion into POPC bilayer, ran 4ns production. is it compulsory to use opls/gromos43a6 *ff for run simulation protein in water? I have repeat to the whole process because wrong usage of depracated *FF.

[gmx-users] RE:Problem about *FF

sudheer babu wrote: > H sudheer babu wrote: > Hi gmx-users, > I used deprecated FF for protein in water simulation and ran > minimisation, equilibration and production. After finishing protein > inserted into POPC bilayer, which has ffgmx.itp. > I thought POPC contain depreca

[gmx-users] Problem about Forcefield

Hi gmx-users, I used deprecated FF for protein in water simulation and ran minimisation, equilibration and production. After finishing protein inserted into POPC bilayer, which has ffgmx.itp. I thought POPC contain deprecated FF similarly I have used same FF for protein in water simlulation also .

[gmx-users] Re: gmx-users Digest, Vol 47, Issue 41

ntents of gmx-users digest..." > > > Today's Topics: > > 1. Problem about *pdbgmx (sudheer babu) > 2. Re: Problem about *pdbgmx (David van der Spoel) > 3. Re: problem with mpi configuration. (Dr. Niharendu Choudhury) > 4. Re:

[gmx-users] Problem about *pdbgmx

Hi gmx-users, I want to protonate only HIS residues in my protein , so I gave command like this *pdb2gmx -f protein.pdb -HIS then it asked which number of HIS to protonate, I gave numbers of HIS residues which I want protonate , it ran fine without error, but when I open conf.gro file, along wit

[gmx-users] Problem of *tpbconv

Hi all, My production run got stopped mid of the simulation, then I tried to generate run inputfile by using *tpbconv for that tag following files used .tpr , .edr and .trr tpbconv -s prt.tpr -f .trr -e .edr -o out.tpr but it's showing error which I pasted below trn version: GMX_trn_file (si

[gmx-users] problem of nvt and npt

Hi gmx-users, I simulated protein in water for 3ns production in NPT condition throughout my simulation, it ran fine. I did n't do NVT at all either in equilibration or production. Will it give bad results if I run in NPT through out simulation? Thanks in advance..

[gmx-users] problem with undistribution of water

Thanks Mr .Justin for your response, I am describing answers for your questions, 1.My box size is 6.0nm in xyz dimensions. 2.The forcefield I am using "ffgmx.itp" for membrane which I downloaded from Pieter Tieleman webiste and deprecated FF for protein. 3 .I inserted protein into membrane by usi

[gmx-users] problem with undistribution of water

Hi gmx users, I inserted my protein into Popc Bilayer . EM is fine, when I do equilibration the water molecules from oneside of bilayer moving to other side, it looks undistribution of water , but total sturucture in cubic form. can you give me detailed information regarding this problem is it due

[gmx-users] problem with trjconv

Hi all, I am trying to use *trjconv command for -pbc but POPC molecules are breaking when visualize in VMD. The commands used are grompp -f pr.mdp -c em_out.gro -p .top -n index.ndx -o out.tpr trjconv -f em_out.gro -s out.tpr -o trj_out.gro -pbc inbox or cluster or whole Thi trj_out.gro con

[gmx-users] peoblem with water

Hi all, I embedded protein into membrane. After that *EM and *PR running fine but in position restrian intial step, one side of the membrane layer, water molecules move to second side although total structure looks cubic form, Only problem with diplacemnt of water to otehrside. Shall I run it for l

[gmx-users] protein in water production run

Hi gmx users, I am doing Protein in water prodcution run , my system is fine till 500ps run, after that when I gave another 250 ps run, job was stopped and shown following error Step 28019, time 56.038 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.17 (between atoms 203 a

[gmx-users] simulation box

Hi gmx-users, I added simulation box by *editconf below mentioned to POPC system downloaded from Tieleman's website, I don't want to add water 1) *editconf -f popc.gro -o popc_box.gro -box 6 6 9 -c this one I followed based on gmx-archives. 2) Then in 2ndcase I used same command but 8 8 8(cubic) i

[gmx-users] problem of general velocities

Hi gmx users, I am doing membrane simulations , In *pr.mdp file kept gen_vel =yes and in * md.mdp file kept " no " , can i use this like or viceversa I tried in different ways. Which way is acceptable. Pls suggest me. ___ gmx-users mailing listgmx-use

[gmx-users] still problem of pr.mdp

Hi gmxusers, i have used below parameters those what you suggested , title = popc restrained define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 1; total 20 ps. nstcomm

[gmx-users] Re: gmx-users Digest, Vol 46, Issue 79

> > Message: 1 > Date: Mon, 25 Feb 2008 06:13:49 -0500 > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] problem about Pr.mdp > To: Discussion list for GROMACS users > Message-ID: <[EMAIL PROTECTED]> > Content-Typ

[gmx-users] problem about Pr.mdp

Thanks Mr.Mark for your reply, I am not getting any error, but after Position restrain step, when I see the structure of *pr_protein_popc_out.gro in VMD the POPC tails are tilting towards backwards(like pulling). It looks there is gap inbetween two membrane layers, middle part of the protein appear

[gmx-users] problem regarding pr.mdp file of protein embedded in popc

Dear gmx-users, I have inserted my protein into membrane. I did energy minimisation with Steepest descent, that output used for input of position restrain, this "EM out.gro" structure is fine . When I do Position restrain, this step goes fine but, popc structure of " PR out.gro " looks tilted.

[gmx-users] Re: gmx-users Digest, Vol 46, Issue 67

ts of gmx-users digest..." > > > Today's Topics: > > 1. Re: Problem regarding tc_grps (Justin A. Lemkul) > 2. problem about position restrain (sudheer babu) > 3. Re: problem about position restrain (Justin A. Lemkul) > 4. Building Topology with all hydrogens

[gmx-users] problem about position restrain

Hi gmx users, I am trying to run position restrain step for protein embedded in popc. is it possible to do position restrain at a time for both popc and protein like below mentioned here? in " .top " file ; Include Position restraint file #ifdef POSRES #include "lip_posre.itp" #include "posre.itp"

[gmx-users] Problem regarding tc_grps

Dear gmx-users, I am working on membrane proteins, I have done position restrain step successfully but, I have doubt about that tc_grps how to use? I have searched in gmx-archives regrading this problem , but I found controversial answers like 1.tc_grps - protein sol Cl

[gmx-users] Re: gmx-users Digest, Vol 46, Issue 56

; 3. Re: problem regarding .top file generated by genbox (Mark Abraham) > 4. RE:problem regarding .top file generated by genbox (sudheer babu) > 5. Re: RE:problem regarding .top file generated by genbox > (Mark Abraham) > > > ---

[gmx-users] RE:problem regarding .top file generated by genbox

Thanks for your reply Mr.justin i am sending the commands and .itp file sequence the command i have used for protein insertion into membrane is genbox -cs lipid.gro -cp protein.gro -p topol.top -o popc_protein.gro , this command was fine it ran without error. Later grompp -f em.mdp -c popc_protein

[gmx-users] problem regarding .top file generated by genbox

HI gmxusers, i am using gromacs version 3.3.1 i am new to gromocs, i was taken protein.top file (which is generated by pdb2gmx). In this file i have included ff.itp , popc.itp and lipid.itp but protein atom types already there (generated by pdb2gmx). This .top file used for inserting of protein int

[gmx-users] problem regarding insertion of protein into lipidbilayer

hi gmx users, i am new to gromacs , i am doing membrane protein simulations. My popc bilayer contain 128 molecules and protein contain 59 aminoacid residues, both systems i have simulated for 1ns . Now i want insert my protein into membrane. I have searched alot in gmxusers for how to insert protei

[gmx-users] problem regarding protein in water simulation

Hi all, my protein contain 59 aminoacid residues and crstal water molecules 103, The steps i have done are 1.minimisation of protein invacuo 2.added simulation box of 6 in xyz dimensions 3.added water 4.added ions 5.energy minimisation in water 6.positoin restrain in water 7.production step..

[gmx-users] problem regarding editconf

hi all, i have one problem regarding 'editconf' for using add simulation box, my protein contain 59 residues + crystal water -103 molecules In one tutorial they have used following command for add simualation box 1.editconf ­bt cubic –f fws.pdb –o fws.pdb –d 0.9- in this 0.9 is nm i have ref

[gmx-users] doubt about constrain

hi gmx users, i have one doubt regarding constriants,i want to do production run of popc in water. In my pr.mdp file i have used constraints of all-bonds, but in case of production which type of constriants i have to use ? i have checked gmx archives some people used "all-bonds" constraints, some p

[gmx-users] problem of pr.mdp file

hi gmx users i have one doubt regarding pr.mdp file of protein.(my protein doesnt contain any missing residues) This protein i have taken after run it in amber. The steps i have done are 1) pdb2gmx conversion 2) Energy minimisation in vaccum Now my doubt is whats the next step ? directly i will

[gmx-users] problem in pr.mdp file

Thanks for response Mr.Alan Dodd 1) 1st run is simularion of position restrain of protein in water (25000 steps) - system running very very slow means for completion 10 steps it is taking more than 5 minutes or more 2) 2nd simulation is production step of popc in water (125000 steps ) - this i

[gmx-users] what is position restrain?

hi gmx users, i have one doubt regarding position restrain, if we want to do postion restrain in amber we mention the atoms in min.in and eq.in files of vaccum phase and in water phase but incase of gromacs where we will mention and more over when we will do postion restrain in gromacs. PR must t

[gmx-users] problem in pr.mdp file

hi gromacs users, iam getting problem while doing postion restrian for the protein system reunning very slow, but i have done md.mdp for another system( bilayer-popc) its running normally, whats the problem in my protein system? i have used pr.mdp file like i am enlosing along with my mail U