Re: [gmx-users] force=nan in frame 0

TED]> To: Discussion list for GROMACS users Sent: Monday, November 12, 2007 2:33:38 PM Subject: Re: [gmx-users] force=nan in frame 0 how do you turn off the interactions? e.g. setting rvdw=0 doesn't mean turning of vdw interactions. Regards, Yang Ye On 11/13/2007 12:55 AM, dongsheng

RE: [gmx-users] force=nan in frame 0

sheng -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Sunday, November 11, 2007 9:04 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] force=nan in frame 0 dongsheng zhang wrote: > Dear Mark, > > Thank you for your

[gmx-users] force=nan in frame 0

) dongsheng zhang wrote: > Hello, > > I have build my own FF for a copolomer. When I ran the program, I got > KE > is NaN. I checked the output file trr. I found the initial forces of all > particles at frame 0 are infinite. Could anyone tell me why this > happened? Where I

[gmx-users] (no subject)

Hello, I have build my own FF for a copolomer. When I ran the program, I got KE is NaN. I checked the output file trr. I found the initial forces of all particles at frame 0 are infinite. Could anyone tell me why this happened? Where I might make a mistake? Thank you in advance! Dongsheng _

Re: [gmx-users] opls parameters

Dear Mark, I think C2 is CH2 group, rather than N atom because of its mass (refer to opls_071, opls_072), and it is said in ffoplsaa.atp that types 1-134 are from the united-atom OPLS. Dongsheng On Sun, 2006-12-03 at 17:20 +1100, Mark Abraham wrote: > > Sorry i'm probably being a bit slow, but

Re: [gmx-users] defining new residues?

It is possible to generate new "residues". First of all, you need to make a decision which force field you will use for your new residues. For example, you will choose opls. then you add one building block into ffoplsaa.rtp. As you read ffoplsaa.rtp, you can see that you need to specify atoms' name

Re: Fwd: [gmx-users] Hi...

On Thu, 2006-09-14 at 13:10 -0700, David van der Spoel wrote: > Dongsheng Zhang wrote: > > On Thu, 2006-09-14 at 06:36 -0700, David van der Spoel wrote: > >> Navratna Vajpai wrote: > >>> Hi all.. > >>> I wrote this mail yesterday. But could not receive an

Re: Fwd: [gmx-users] Hi...

On Thu, 2006-09-14 at 06:36 -0700, David van der Spoel wrote: > Navratna Vajpai wrote: > > Hi all.. > > I wrote this mail yesterday. But could not receive any reply till now. > > So if someone can suggest something about it. That would be nice. > > Best regards > > Nav > > > > Begin forwarded m

Re: [gmx-users] RE: opls

Hello, I believe this question has been asked several times. It is true that ffoplsaabon.itp misses some parameters for dihedral for the capped residues (ACE NAC). I think you can add some estimated values to the ffoplsaabon.itp, or ignore the warnings. All the best! Donnsheng On Sat, 2006

[gmx-users] segmentation fault

Dear GMX users, I am studying adsorption of polymers on a surface. I want to enforce all polymers to be adsorbed, so I increase 10 times of the LJ interaction between polymers and the surface, then I got segmentation fault. Without increasing, the program ran fine (some polymers are not adsorbed)

Re: [gmx-users] mdrun hangs on nodes of P655+ aix 5.2

s tree. > > However, I think we made the 3.3.1 release after march 9, in which > case it is included there. > > Cheers, > > Erik > > On Aug 5, 2006, at 12:05 AM, Dongsheng Zhang wrote: > > > Dear Erik, > > > > I had the same problem

Re: [gmx-users] mdrun hangs on nodes of P655+ aix 5.2

wrote: > Hi, all, > > I was able to fix the problem by: > > 1) Reducing my PME order from 6 to 4 > 2) Reducing my Fourier spacing from 0.12 to 0.06 > 3) Also, I had to do comm_grps = System or comm_grps = > Protein > > Best wishes, > Art > > --- Dongsheng Zh

Re: [gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Dear Erik, I had the same problem as Arthur Roberts. So I downloaded your new version of gmx_system_xdr.h and gmx_system_xdr.c from http://bugzilla.gromacs.org/show_bug.cgi?id=55 Before I recompile gromacs, I checked the difference between your new version and the old one. The result is as follow

Re: [gmx-users] Langevin dynamics ( Large VCM )

If you want to use BD, the friction coefficient has to be large. Please check the manual. If you change your bd-fric to 5000, it might help. On Wed, 2006-08-02 at 23:24 +0800, PAUL NEWMAN wrote: > Hi: > Thanks to everybody who helped me out with my last email. But now I > have another problem a

RE: [gmx-users] segmentation fault, very high KE but no high velocity

On Thu, 2006-07-20 at 14:55 +0200, Berk Hess wrote: > > > >From: Dongsheng Zhang <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users > >To: Discussion list for GROMACS users > >Subject: RE: [gmx-users] segmentation fault, very high KE but n

RE: [gmx-users] segmentation fault, very high KE but no high velocity

best! Dongsheng On Thu, 2006-07-20 at 09:20 +0200, Berk Hess wrote: > > > >From: Dongsheng Zhang <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users > >To: Discussion list for GROMACS users > >Subject: [gmx-users] segmentation fault, very high

[gmx-users] segmentation fault, very high KE but no high velocity

Hello, gmx users, I got segmentation fault during a simulation. I outputted log, xtc, trr file every step. From the log file, I can see that the KE is very high in the last step, so I checked the velocities of particles in the last step. Surprisingly there is no particle whose absolute value of th

Re: [gmx-users] g_bond

error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! Could you please tell me where is the error? Thank you! Dongsheng On Wed, 2006-07-19 at 08:40 +0200, David van der Spoel wrote: > Dongsheng Zhang wrote: > > Hello, GMX users, > > > > When I tried to use g_bond -f *

[gmx-users] g_bond

Hello, GMX users, When I tried to use g_bond -f *xtc -n *.ndx to get a bond length, I got an error message as follows: Fatal error: No distribution... (i0 = 999, i1 = 1)? ? ! ! ? ! Could someone tell me what that means? Thank you in advance! Dongsheng ___

[gmx-users] segmentation fault

Dear GMX users, My system is PEO-PPO-PEO triblock polymers with a coarse grained force field. The nonbonded interactions are tabulated. The interaction range in my tables in 5 nm. The cutoff is 1.4 nm. The table extention is 2 nm. If I simulation only one chain, it works fine. However, the program

Re: [gmx-users] program crashes when -table option used

approach, could you please tell me how to modify it? All the best! Dongsheng On Fri, 2006-07-14 at 10:23 +0200, Berk Hess wrote: > > > >From: Dongsheng Zhang <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users > >To: Discussion list for GROMACS use

Re: [gmx-users] program crashes when -table option used

> > Yang Ye > > Dongsheng Zhang wrote: > > Dear GMX users, > > > > > > I have a coarse-grained model whose nonbonded potentials are tabulated, > > so I have to use user defined potential in gromacs. With Yang Ye's great > > help, I can impl

[gmx-users] program crashes when -table option used

Dear GMX users, I have a coarse-grained model whose nonbonded potentials are tabulated, so I have to use user defined potential in gromacs. With Yang Ye's great help, I can implement the new force field. However, the program always crashed because of Large VCM(group rest). I have done a test by r

Re: [gmx-users] coarse-grained model

> > > > > > Dongsheng > > > > > > On Wed, 2006-07-12 at 11:18 +0800, Yang Ye wrote: > > > >> Don't worry about that. > >> mdrun -tablep {tablep} will follow the scheme {tablep}_A_A.xvg, > >> {tablep}_B_B.xvg ... > >>

Re: [gmx-users] coarse-grained model

laced by your own filename. > > Yang Ye > > Dongsheng Zhang wrote: > > Yang ye, > > > > Thank you very much. > > > > I have three different monomers in my system, so I have 6 different > > regular VMDs and 6 different 1-4 interactions. C

Re: [gmx-users] coarse-grained model

C A14 A14 B14 B14 C14 C14 A14 B14 A14 C14 B14 C14 If I set as the above, I wonder how gromacs know the last 6 table is for 1-4 interaction. All the best! Dongsheng On Wed, 2006-07-12 at 09:54 +0800, Yang Ye wrote: > mdrun -tablep > > Dongsheng Zhang wrote: > > Hello, GMX users,

[gmx-users] coarse-grained model

Hello, GMX users, I have a coarse-grained model. Both 1-4 and regular vdw interaction are tabulated, but no electrostatic interaction. Since there is no entry for 1-4 interaction in energy_table. I am thinking to fool gromacs by treating 1-4 interactions as electrostatic interactions, in other wor

Re: [gmx-users] proper dihedrals

Those parameters should be in **bond.itp file, and you can use four atoms to define a dihedral angle. You can check ffoplsaabon.itp. I am confused by that note as well. On Tue, 2006-07-11 at 13:14 -0400, ARGYRIOS KARATRANTOS wrote: > Hi all, > > according to the manual the proper dihedrals ar

Re: [gmx-users] how to interpretate a tpr file

:58 +0800, Yang Ye wrote: > > > >> Dongsheng Zhang wrote: > >> > >>> Yang Ye, > >>> > >>> Thank you very much for your help. I still have some questions: > >>> > >>> On Mon,

Re: [gmx-users] how to interpretate a tpr file

On Mon, 2006-07-10 at 13:58 +0800, Yang Ye wrote: > Dongsheng Zhang wrote: > > Yang Ye, > > > > Thank you very much for your help. I still have some questions: > > > > On Mon, 2006-07-10 at 11:35 +0800, Yang Ye wrote: > > > >> Dongs

Re: [gmx-users] how to interpretate a tpr file

Yang Ye, Thank you very much for your help. I still have some questions: On Mon, 2006-07-10 at 11:35 +0800, Yang Ye wrote: > Dongsheng Zhang wrote: > > Dear GMX users: > > > > > > Could someone help me to understand these information from a position > > restrai

[gmx-users] use both LJ and buckingham potential for nonbonded potential

Dear gmx users, I find a force field that uses both LJ and Buckingham potential for different nonbonded potentials. I would like to use it in gromacs. I have try it, gromacs gave me a fatal error: ERROR 1 [file "ffpolymernb.itp", line 49]: Trying to add Buck.ham (SR) while the default nonbond ty

[gmx-users] how to interpretate a tpr file

Dear GMX users: Could someone help me to understand these information from a position restrained tpr file? 1. excl[0][0..17]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 18, 26, 28} 2. blocks[CGS][0][0..19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,

Re: [gmx-users] Error

You can use gmxdump to check what's inside your xtc file. This may help you figure out what's going on. On Fri, 2006-07-07 at 19:03 +0200, karamyog singh wrote: > Dear Users, > When I try and convert my traj.xtc file to a .gro file I get the > following error > > Reading frame 0 time0

[gmx-users] program crash

Dear GMX users, My program crashed very soon after it started. I had done EM, and the conformation looked fine in VMD. When I investigated what's wrong, I outputted the coordinates, forces, velocities and log file in every step. I set some parameters in mdp file as follows: gen_vel

Re: [gmx-users] high initial temperature with low ref_T

Dear Mark, Do you have any idea what's wrong with my simulation? You can find the mdp file and the description how I set up my system at the bottom of this email. All the best! Dongsheng On Thu, 2006-07-06 at 19:16 -0400, Dongsheng Zhang wrote: > Mark, > Thank you very much for

RE: [gmx-users] high initial temperature with low ref_T

On Fri, 2006-07-07 at 09:02 +1000, Dallas B. Warren wrote: > > My system exploded very soon after mdrun. So I outputted the > > log file every step. I found the initial temperature is about > > 800 K even though I set ref_T = 300. Why does this happen? > > What temperature did you specify when g

Re: [gmx-users] high initial temperature with low ref_T

Mark, Thank you very much for your reply. On Fri, 2006-07-07 at 08:51 +1000, Mark Abraham wrote: > > Hello, GMX users, > > > > My system exploded very soon after mdrun. So I outputted the log file > > every step. I found the initial temperature is about 800 K even though I > > set ref_T = 300. Wh

[gmx-users] high initial temperature with low ref_T

Hello, GMX users, My system exploded very soon after mdrun. So I outputted the log file every step. I found the initial temperature is about 800 K even though I set ref_T = 300. Why does this happen? The following is from my mdp file: tau_t= 0.1 0.1 ref_t

[gmx-users] tpr file

Dear GMX users, The following message is from a tpr file by gmxdump command: atom[ ]={type= 4, typeB= 4, ptype=Atom, m= 1.20110e+01, q=-5.29400e-01, mB= 1.20110e+01, qB=-5.29400e-01, resnr= 32} grpnrs=[ 0 0 0 0 0 0 0 0 0 0 ]} Could anyone tell me what does "type= 4" mean? I have ch

Re: [gmx-users] program crashed

Mark, I have written a new force field for my polymer. I have used this force field for polymer in water. It worked fine. When I tried to put polymer with nanotube in water, then I had this strange problem (My force field worked fine for nanotube alone). Anyway I will try to rerun it. Thank you f

Re: [gmx-users] program crashed

On Wed, 2006-07-05 at 15:11 +1000, Mark Abraham wrote: > > Mark, > > > > Thank you for your reply. When I checked step38885.pdb, I found a > > polymer chain in my system fall apart (bond broken). If I visualize the > > trajectory. it is fine till step38000 (last frame in my trr file). > > OK...

Re: [gmx-users] program crashed

Mark, Thank you for your reply. When I checked step38885.pdb, I found a polymer chain in my system fall apart (bond broken). If I visualize the trajectory. it is fine till step38000 (last frame in my trr file). I don't understand why the bond breaks after 76 ps simulation and why KE doubles sudde

Re: [gmx-users] program crashed

1184 89.90.8390 0.1510 0.1090 1182 1185 57.30.1093 0.1129 0.1090 1242 1245 61.10.1090 0.1092 0.1090 Thank you for your help! Dongsheng On Tue, 2006-07-04 at 09:52 -0400, Dongsheng Zhang wrote: > mark, > > That is a good idea. Thank you

Re: [gmx-users] program crashed

mark, That is a good idea. Thank you very much! Dongsheng On Tue, 2006-07-04 at 15:38 +1000, Mark Abraham wrote: > Dongsheng Zhang wrote: > > Mark, > > > > Thank you for your reply. EM works fine before position-restrained MD. > > Do you have any other suggestion b

Re: [gmx-users] program crashed

Mark, Thank you for your reply. EM works fine before position-restrained MD. Do you have any other suggestion besides to reduce the number of water inside the nanotube? Thanks! Dongsheng On Tue, 2006-07-04 at 15:23 +1000, Mark Abraham wrote: > Dongsheng Zhang wrote: > > Dear

[gmx-users] program crashed

Dear GMX users, I am studying a system of a capped nanotube with a polymer in water. When I use genbox, some water will be inside of the nanotube. This might cause bad contact of water molecules inside of nanotube. Does anyone know how to control the total number of water molecules inside the nano

[gmx-users] oplsaa force field

Dear GMX users, I'd like to use oplsaa FF format to build my own force field for my project. After I finished it, I can use pdb2gmx. but not grompp. The problem is from my **nb.itp file. I have specified some unusual (not follow the combination rule) nonbonded interaction parameters after [ atomty

[gmx-users] oplsaa force field

Dear GMX users, In ffoplsaanb.itp, there are 8 columns. ; name bond_typemasscharge ptype sigma epsilon opls_001 C 6 12.01100 0.500 A3.75000e-01 4.39320e-01 ; SIG In ffG53a5nb.itp, there are 7 columns. [ atomtypes ] ;name at.num mass charge

[gmx-users] tpbconv

Hello, GMX users, I was running a parallel MD simulation, the program stopped (no more output data) in the middle without any error message in the log file. When I use command "top" to check the process, the output message showed the program was still running, but no more output data. Therefore I

Re: [gmx-users] no more output data from a simulation

Hi, > > The serial version of mdrun defaults to nice 19, i.e. it only runs > when nothing else wants the CPU. Check if something else is running! > > Cheers, > > Erik > > On Jun 27, 2006, at 8:12 PM, Dongsheng Zhang wrote: > > > Dear GMX users, > >

[gmx-users] no more output data from a simulation

Dear GMX users, I have run a simulation several days ago. It supposed to finish on Sunday. However, the program seems stop in the middle. There is no more output. If I use command "top" to check the process, it shows the program is still running. And there is no error message in the log file eithe

Re: [gmx-users] xyz to gdb

Hello, Jason, You can download babel program and use babel -ixyz old.xyz -opdb new.pdb to get a pdb file, then you can use gromacs now. Dongsheng On Mon, 2006-06-26 at 15:00 -0700, Jason Byrd wrote: > Hello, > > I amd working with using the Siesta program in conjunction with > gromacs, and I

Re: [gmx-users] make_ndx

Hello, Manuel, Thank you very much for your trick. It is neat. Have a nice weekend! Dongsheng On Sun, 2006-06-25 at 02:58 +0200, Manuel Prinz wrote: > Hello Dongsheng! > > Am Samstag, den 24.06.2006, 17:26 -0400 schrieb Dongsheng Zhang: > > In make_ndx, I would like to keep

[gmx-users] make_ndx

Hello, gmx users: In make_ndx, I would like to keep two groups, for instance, group 4 and group 5. I have try it in two ways, namely, "keep 4 & keep 5" and "keep 4 | keep 5". However both ways only keep group 4. Anyway to accomplish my task is to delete other groups one by one, but it is not so c

Re: [gmx-users] energy minimization

Hi, David, Thank you for your help. I have fix it now. Have a nice weekend! Dongsheng On Sat, 2006-06-24 at 21:53 +0200, David van der Spoel wrote: > Dongsheng Zhang wrote: > > Hello, everyone, > > > > I have a system with a nanotube and a polymer chain. First I did EM

[gmx-users] energy minimization

Hello, everyone, I have a system with a nanotube and a polymer chain. First I did EM for the system in vacuum. After that, I added some water to my system, and tried to do EM again. This time I got some large force on some atoms. The messages are as folllows: Step=0, Dmax= 5.0e-03 nm, Epot= -

Re: [gmx-users] a strange behavior in editconf -rotate

Dear Tsjerk, Thank you very much for your reply. You are right. After I specify pbc=no in mdp file, EM works fine for test2.pdb now. All the best! Dongsheng On Fri, 2006-06-23 at 08:19 +0200, Tsjerk Wassenaar wrote: > Hi Dongsheng Zhang, > > Rotating the system with editconf

[gmx-users] a strange behavior in editconf -rotate

Dear GMX users, I have generated a pdb file (test1.pdb) for a PPO chain. I can do energy minimization for this chain using oplsaa FF. However, if I rotate the chain by editconf -f test1.pdb -rotate 9 -9 0 -o test2.pdb then I can't do EM for test2.pdb. Could anyone tell me why the rotation of a

Re: [gmx-users] unexpected result from mdrun

7;re not exactly identical? Did you try gmxdump and then diff > the output? > > David > > On 6/19/06, Dongsheng Zhang <[EMAIL PROTECTED]> wrote: > > Dear GMX users, > > > > I have two EXACTLY identical tpr files at two different directories on > > the SAM

Re: [gmx-users] unexpected result from mdrun

, 2006-06-19 at 14:52 -0400, Dongsheng Zhang wrote: > Dear GMX users, > > I am studying the interaction between a polymer chain and a nanotube in > vacuum. After I set up my system, I use vmd to visualize my gro file. It > looks fine. The polymer chain is a little far away from the na

[gmx-users] unexpected result from mdrun

Dear GMX users, I am studying the interaction between a polymer chain and a nanotube in vacuum. After I set up my system, I use vmd to visualize my gro file. It looks fine. The polymer chain is a little far away from the nanotube. There is no overlap. However, after I do mdrun, I can't get edr fil

Re: [gmx-users] grompp error:Invalid order for directive defaults

used oplsaa to get my cnt.itp, that's the reason I need two defaults sections. Best Wishes! Dongsheng On Mon, 2006-06-12 at 17:20 +0200, David van der Spoel wrote: > Dongsheng Zhang wrote: > > Dear David, > > > > Thank you very much for your reply. I am sorry to t

Re: [gmx-users] special molecule

Sear Mark, Since PRODRG server only generates a itp file by using gromos type force field, do I have to use gromos force field for my whole protein-ligand system if my ligand force field parameters are got from PRODRG? In another word, can I mix two different force field (one for protein, one for

Re: [gmx-users] special molecule

I think you can use editconf to convert your original pdb to a gro file. On Mon, 2006-06-12 at 13:48 +, Tamas Horvath wrote: > As I understand, if there are "special" molecules in a pdb file, > pdb2gmx cannot convert it. However, PRODRG can create an *.itp file > for that molecule, so that I

Re: [gmx-users] grompp error:Invalid order for directive defaults

t 09:35 +0200, David van der Spoel wrote: > Dongsheng Zhang wrote: > > Dear GMX users, > > > > I'd like to study the interaction between carbon nanotube and a polymer > > chain. I have made cnt.itp for the nanotube and poly.itp. Both itp files > > cont

[gmx-users] grompp error:Invalid order for directive defaults

Dear GMX users, I'd like to study the interaction between carbon nanotube and a polymer chain. I have made cnt.itp for the nanotube and poly.itp. Both itp files contains force field parameters (such as [ defaults ], [ atomtypes], [ bondtypes ]), in this way, I don't need to include any force field

Re: [gmx-users] REMD in one nodes with two processors

#x27;t work. Thank you very much for your help! Dongsheng On Thu, 2006-05-04 at 21:52 +0200, David van der Spoel wrote: > Dongsheng Zhang wrote: > > Thank you, David. I try it as: > > > > > > mpirun -np 2 n1 /home/brasilia/dong/mdrun_mpi -replex 500 -reseed >

Re: [gmx-users] REMD in one nodes with two processors

van der Spoel wrote: > Dongsheng Zhang wrote: > > Dear David, > > > > I had tried mpirun before, it didn't work either. the command was: > > mpirun -np 2 n1 /home/brasilia/dong/mdrun_mpi_MC -replex 500 -reseed -1 > > -multi -s replica -deffnm replica -N 2 -v

Re: [gmx-users] REMD in one nodes with two processors

5-04 at 19:13 +0200, David van der Spoel wrote: > Dongsheng Zhang wrote: > > Marcus, > > > > Thank you for your suggestion. I try it. The computer gives me the same > > error message. The problem is that the program always looks for > > replica.tpr instead of replica

Re: [gmx-users] REMD in one nodes with two processors

itzki wrote: > If you use the -deffnm option, you do not need -s, b/c it is > already accounted for with the -deffnm. > Marcus > > Dongsheng Zhang wrote: > > David, > > > > Thank you for your reply. I have provided replica0.tpr and replica1.tpr, > > but the pr

Re: [gmx-users] REMD in one nodes with two processors

doesn't work either (complains only one replica: Nothing to exchange with only one replica). it seems the program does not recognize the -multi option. Best wishes! Dongsheng On Thu, 2006-05-04 at 18:11 +0200, David van der Spoel wrote: > Dongsheng Zhang wrote: > > Dear gmx u

[gmx-users] REMD in one nodes with two processors

Dear gmx users, I have trouble to run REMD on one node with two processors. The command I used is /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi -s replica -deffnm replica -N 2 -v >& zevel the error message is: Can not open file: replica.tpr This error message looks strange

Re: [gmx-users] REMD

\n \n", p_max,lincsd->bla[2*p_imax]+1,lincsd->bla[2*p_imax+1]+1,p_rms); } I have a question about these codes, why does the output process stop in the middle? (Disk space is very large, not full) thank you for your help! Dongsheng On Thu, 2006-04-13 at 16:13 +020

Re: [gmx-users] REMD

Dear David, I forgot one more information. The computer administrator told me I did not need to use mpirun. As I told you in the previous email, I have done tests for parallel computing. It worked fine. Dongsheng On Thu, 2006-04-13 at 09:52 +0200, David van der Spoel wrote: > Dongsheng Zh

Re: [gmx-users] REMD

need more information, please let me know. Thank you very much for your help! Best Wishes! Dongsheng On Thu, 2006-04-13 at 09:52 +0200, David van der Spoel wrote: > Dongsheng Zhang wrote: > > dear Mark, > > > > Thank you very much for your prompt reply. I try to use paral

Re: [gmx-users] REMD

dear Mark, Thank you very much for your prompt reply. I try to use parallel computing. It works fine. for example: grompp -f -c -p -o replica0 -np 2 -sort -shuffle to get replica0.tpr then, mdrun_mpi -np 2 -s replica0.tpr The error message mentioned in the previo

[gmx-users] REMD

Dear gmx users: I am trying to run REMD with two replicas (for testing). I used grompp -f -c -p -o replica0 to get replica0.tpr grompp -f -c -p -o replica1 to get replica1.tpr then used mdrun_mpi -np 2 -multi -replex 500 -reseed -1 -s replica -deffnm replica -v -N 2 to run it. I got an error me

[gmx-users] modifying replica exchange

Dear gmx developer, I want to modify repl_ex.c for my system. I have read the source code. There is one point I am not clear. In the function replica_exchange( ...), all dynamical information of a system will be exchanged between two replicas when exchanging two replicas is implemented. It looks l

[gmx-users] how to do simulation at high temperature

Dear gmx users, I want to simulate a short peptide in solution at high temperature (e.g. T=800). Because of the large momentum of molecules, it is very easy to have bad contacts to cause the system to crash. One way to prevent it is to reduce the time step. Therefore I have tried to use dt=0.0005

Re: [gmx-users] pdb2gmx illegal instruction

Dear Tom, Thank you for your reply. Unfortunately, mpirun is not available. I can only find mdrun_mpi which is related with mpi. Best wishes! Dongsheng On Tue, 2006-03-21 at 21:02 -0500, Tom Joseph wrote: > Certainly you should consult your documentation, but one possibility is: > > mpiru

Re: [gmx-users] pdb2gmx illegal instruction

Dear Erik, Thank you very much for your help. When I check command under ../bin directory, I only find mdrun_mpi (which is related mpi), not mpirun. I have tried mpirun (because I find some people used mpirun in the mailing list), the computer complained "mpirun not found". Could you please tell

Re: [gmx-users] pdb2gmx illegal instruction

optimized for) one machine, > but run another. Give us some info both about the command you ran and > how Gromacs was compiled/installed. > > Cheers, > > Erik > > On Mar 21, 2006, at 6:11 AM, Dongsheng Zhang wrote: > > > Dear All, > > > > I

Re: [gmx-users] pdb2gmx illegal instruction (core dumped)

Dear David, Thank you very much for your quick reply. The machine is IBM. Then, could you please tell me how to fix it? Thanks again. Best Wishes! Dongsheng On Tue, 2006-03-21 at 17:00 +0100, David van der Spoel wrote: > Dongsheng Zhang wrote: > > Dear All, > > > > I w

[gmx-users] pdb2gmx illegal instruction (core dumped)

Dear All, I want to use gromacs in research computing center in my school. When I used pdb2gmx as pdb2gmx -f Ace5AlaNac -o Ace5AlaNac -p Ace5AlaNac -ignh -ter it gave me an error message as follows, illegal instruction (core dumped) Could anyone give me a clue what is wrong? Thank you in advance

[gmx-users] pdb2gmx illegal instruction

Dear All, I want to run gromacs in supercomputer center at my school. When I used pdb2gmx, it gave me an error message as follows: illegal instruction (core dumped out) Could anyone give a clue what's happening? Thank you in advance. Dongsheng ___ gmx

[gmx-users] g_covar

Hello, everyone, I have finished a MD simulation of a short peptide. The initial conformaton of my peptide is the extended conformation, soon the peptide changed to be a helix and kept it for a long time. I would like to use g_covar to analyze my simulation with a helix conformation as my referenc

[gmx-users] grompp -check14

Dear all, Has anyone used -check14 for grompp? When I tried it just now, I got segmentation fault. grompp works fine without the option -check14 (or with the option -nocheck14). The error message is as follows: grompp -f md01.mdp -c ala5 -p ala5 -check14 -o full Back Off! I just backed up mdout.m