[gmx-users] gromacs

Dear all, I download gromacs-4.0.5 and installed it. I got the test by git. git clone git://git.gromacs.org/regressiontests.git then: Testing fe_test . . . PASSED Testing field . . . FAILED. Check checkvir.out (264 errors) files in field Testing nacl . . . PASSED Testing sw . . . PASSED Test

[gmx-users] Re: gromacs

All 63 kernel tests PASSED Here follows a list of the lines in reference_s.log and ener.log which did not pass the comparison test within tolerance 0.05 Index Reference This test Error Description 11-34.5967-42.0952 0.0977748 1aml.pdb with G53a6 using vsite=none and water=spc

Re: [gmx-users] Re: gromacs

These messages are characteristic of correctly-functioning GROMACS. This is why using the test set is not encouraged. See http://www.gromacs.org/index.php?title=Download_%26_Installation/Test-Set for links with more information. Also, why bother doing a fresh install of a GROMACS version tha

[gmx-users] potential calculation

Dear all, is there a way to calculate patencial energy at a user defined point in a simulation box. Thanks, Peicho.-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Plea

Re: [gmx-users] potential calculation

From a trajectory energy file (file extension edr) you can extract different component of the potential energy using the program g_energy. Have a look at the manual and instructions given by g_energy -h. On Apr 21, 2010, at 11:01 AM, Peicho Petkov wrote: Dear all, is there a way to calculat

[gmx-users] simulated annealing

Hi gromacs users I want to use simulated annealing. I have a question: 1) in mdp file, T-couple = no. is that true? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! P

[gmx-users] can't see bonds between my CG beads in VMD

Hi all, I am running coarse grain MD simulations first time and unable to see bonds after loading .gro and .trr file in vmd. I have made initial .pdb by atom2cg.awk, then .itp by seq2itp.pl. With use of this, I prepared .pdb ,.itp and .top and subjected to mdrun. During analysis in vmd I can't see

[gmx-users] simulated annealing

Hi gromacs users it is my mdp file: annealing: single annealing_npoints: 5 annealing_time: 0 3 6 9 12 annealing_temp: 500 450 400 350 300 300 is my ref-t. is it true? Thank you so much for any help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/lis

Re: [gmx-users] can't see bonds between my CG beads in VMD

swapnil chavan wrote: Hi all, I am running coarse grain MD simulations first time and unable to see bonds after loading .gro and .trr file in vmd. I have made initial .pdb by atom2cg.awk, then .itp by seq2itp.pl . With use of this, I prepared .pdb ,.itp and .top and subje

Re: [gmx-users] simulated annealing

leila karami wrote: Hi gromacs users I want to use simulated annealing. I have a question: 1) in mdp file, T-couple = no. is that true? No. You need a thermostat to control the temperature of your system. -Justin -- Justin A. Lemkul Ph.D. Ca

Re: [gmx-users] simulated annealing

leila karami wrote: Hi gromacs users it is my mdp file: annealing: single annealing_npoints: 5 annealing_time: 0 3 6 9 12 annealing_temp: 500 450 400 350 300 300 is my ref-t. is it true? The value of ref_t doesn't matter so much, since, according to the manual: "The actual a

[gmx-users] simulated annealing

Dear Justin thanks for your attention I want to use simulated annealing to obtain global minimum for protein-dna structure. I will do first heating and then slowly cooling. is my mdp file true, now? T-couple = brendsen ref-t = 300 annealing: single annealing_npoints: 5 annealing_time: 0 3

Re: [gmx-users] simulated annealing

leila karami wrote: Dear Justin thanks for your attention I want to use simulated annealing to obtain global minimum for protein-dna structure. I will do first heating and then slowly cooling. is my mdp file true, now? T-couple = brendsen ref-t = 300 annealing: single annealing_npo

[gmx-users] Atom Type not found............

HI i have generated a topology file for drug using prodrg with gromos 96.1force field , now i want to use it for simulation with DNA in complex. I am using amber 03 force field for my system . i have included correctly the drg.itp file in generated topology file for DNA alone (using pdb2gmx). i

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

PAVAN PAYGHAN wrote: HI i have generated a topology file for drug using prodrg with gromos 96.1force field , now i want to use it for simulation with DNA in complex. I am using amber 03 force field for my system . i have included correctly the drg.itp file in generated topology file for D

[gmx-users] simulated annealing

Dear Justin thanks for your accuracy. I want to use simulated annealing to obtain global minimum for protein-dna structure. I will do first heating and then slowly cooling and I will my full md simulation in 300K. is my manner true? if so, is my mdp file true, now? Tcouple = berendsen ref_t = 300

Re: [gmx-users] genbox

shahid nayeem wrote: I was also trying to put more than one protein in one simulation box. I was able to do it with genconf but it appears that the addition is in very ordered manner if one looks .gro file in VMD. How can I add these protein in disordered random orientation. That's certainl

Re: [gmx-users] genbox

I was also trying to put more than one protein in one simulation box. I was able to do it with genconf but it appears that the addition is in very ordered manner if one looks .gro file in VMD. How can I add these protein in disordered random orientation. msnayeem On 4/20/10, Justin A. Lemkul wro

Re: [gmx-users] simulated annealing

On 21/04/2010 10:19 PM, leila karami wrote: Dear Justin thanks for your accuracy. I want to use simulated annealing to obtain global minimum for protein-dna structure. I will do first heating and then slowly cooling and I will my full md simulation in 300K. is my manner true? if so, is my mdp fil

Re: [gmx-users] how to use altivec on power6 cpu

On 21/04/2010 4:14 PM, shuqi zhao wrote: Dear all, I am compiling gromacs 4.0.7 on AIX 5.3 with "./configure --enable-mpi --enable-ppc-sqrt=1 --enable-ppc-altivec --disable-fortran --with-fft=fftw3". The source codes under src/gmxlib/nonbonded/nb_kernel_ppc_altivec/ are compiled and archived. How

[gmx-users] parallel simulation in dual core PC

Hi, I compare the run times. The calculation of two processors is faster than one. And I saw the utility of the two cores large than 85% separately. I can sure it's exactly parallel simulation in my PC now. Another question is: someone told me the interconnect, 1G Ethernet, of the machine in our

Re: [gmx-users] parallel simulation in dual core PC

On 21/04/2010 11:29 PM, Hsin-Lin wrote: Hi, I compare the run times. The calculation of two processors is faster than one. And I saw the utility of the two cores large than 85% separately. I can sure it's exactly parallel simulation in my PC now. Another question is: someone told me the interco

[gmx-users] The problems of controling one atom through modify gromacs sourse code

Hi,gmx-users, Now I want to control the motion of a certain atom (due to special needs).So I added some codes like "if(n==my_atom)xprime[n][d] = x[n][d]+...;" in the functionstatic "void do_update_md()" of the file "gromacs-4.0.7\src\mdlib\update.c".But when mpi run,The gromacs performs a

[gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations

Hi, I moved this to the user list, so it will be of use to others. I have no clue what you are trying to do, what groups you are accelerating or freezing. So we can't help you without further information. Setting up simulations with frozen groups, accelerate groups or different coupling temper

Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations

Dear Berk, I am sorry for poor communication, Herewith i am giving my md.mdp file. I this file as you could see i am using two temp coupling groups Tmp1 is protein and a 2nm spherical layer of water around it, and the second one Tmp2 which has only water. Now i want to fix the Tmp2 and apply 0 K t

[gmx-users] free energy : query on constraint force pull code

Hi, I would like to use constraint force pull code to calculate the free energy of association of two peptide using the distance between center of mass of two peptides as reaction coordinate. I am planning to use gromacs 4. Here I have some queries: 1. Since I will constraint method, I guess,

Re: [gmx-users] parallel simulation in dual core PC

Did you preprocess the .tpr file for 2 cores with grompp? Also, I believe you have to have an additional -np 2 after the mdrun_mpi command: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c 200ns.gro -np 2 -- at least this is what I understand from what my prof told me.

Re: [gmx-users] parallel simulation in dual core PC

Arden Perkins wrote: Did you preprocess the .tpr file for 2 cores with grompp? Also, I believe you have to have an additional -np 2 after the mdrun_mpi command: mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log -c 200ns.gro -np 2 -- at least this is what I understand

[gmx-users] Postdoctoral position in BCAM

Dear All, Since in my group we are using intensively GROMACS code and its modifications, I think that this would be a right place to advertise a new opening in the Basque Centre for Applied Mathematics (BCAM) in the Hybrid Monte Carlo (HMC) simulations group http://www.bcamath.org/public_job/c

[gmx-users] help(Free Energy)

-- Shikhar Gupta Senior Research Fellow Pharmacoinformatics Department Block- A (Room No.- 208) National Institute of Pharmaceutical Education & Research( NIPER ) Sec- 67, S.A.S Nagar Mohali, Punjab (India) Web-Site: www.niper.ac.in PIN- 160062 Email:shik_...@rediffmail.co

Re: [gmx-users] help(Free Energy)

shikhar gupta wrote: Hi gmx users, I used g_lie command to compute free energy. The command and the output is as follow [shik...@venus 30078-dyn10ns]$ g_lie -f edr.edr -ligand UNK -o lie10ns.xvg -ligand string UNK Name of the ligand in the energy file Opened edr.edr as single precision en

Re: [gmx-users] parallel simulation in dual core PC

On 22/04/2010 3:12 AM, Arden Perkins wrote: Did you preprocess the .tpr file for 2 cores with grompp? This was only necessary for GROMACS 3. Also, I believe you have to have an additional -np 2 after the mdrun_mpi This was only necessary with early versions of MPI libraries. command: mpir

[gmx-users] warning when process the files with grompp

 Hello, I want to generate the em.tpr file, but  it arise the warning like this : Warning: atom name 1 in TBP_wat.top and 10tbpc12wat1.gro does not match (C13 - OW) Warning: atom name 2 in TBP_wat.top and 10tbpc12wat1.gro does not match (C10 - HW1) Warning: atom name 3 in TBP_wat.top and 10tbpc1

RE: [gmx-users] warning when process the files with grompp

It is most likely due to having the order of your molecules in the topology file (.top) different to those that are in coordinate file (.gro). Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Pa

[gmx-users] g_rama, g_chi for polymer structure

Dear gmx-users, I want to construct the Ramachandran Plot for the molecules I am simulating -- 100 polyethylene chain (n=16). But when I do $ g_rama, I get "Found 0 phi-psi combinations" message. The problem seems to me that when I ran the simulation initially, I didn't have dihedral information l

Re: [gmx-users] g_rama, g_chi for polymer structure

On 22/04/10 15:09, Yongchul Chung wrote: Dear gmx-users, I want to construct the Ramachandran Plot for the molecules I am simulating -- 100 polyethylene chain (n=16). But when I do $ g_rama, I get "Found 0 phi-psi combinations" message. The problem seems to me that when I ran the simulation init