Re: [gmx-users] Time unit issue with g_anaeig

On 14/11/2011 5:46 PM, Kei Sit wrote: Hi all, I'm new to gromacs so I hope I haven't done something wrong that is extremely simple. I have recently been using gromacs to analyse an MD trajectory using g_covar and g_anaeig. I have output saved to the trajectory every ps and I currently have a

[gmx-users] orca and Segmentation fault

dear sir :  I installed gromacs-orca for qm/mm ./configure --without-qmmm-orca --with--qmmm-gaussian --enable-mpi make make install MPI is lam-mpi   when run mdrun , the error " Back Off! I just backed up md.log to ./#md.log.12# Getting Loaded... Reading file pyp.tpr, VERSION 4.5.1 (single pre

[gmx-users] Problem about simulation at high temperature and ratio of sencondary stuctures

Hi Gromacs users, I am using GROMACS (ver4.5.3) to run molecular dynamics (MD) simulation. However during my simulation runs, I encountered some problems as stated below: 1. In NPT condition, the box size undergoes changes, especially at high temperature simulations. However, during semisot

[gmx-users] Atomtype 'CR' not found

Hiii All... I want to do steepest descent energy minimization for molecule Bromobenzisoxazolone Barretin, I have all the required files like.itp and .gro. Also, changed force field from ffG43a1 to ffgmx but no use. Same error of Atomtype 'CR' not found, is coming again n again. Please suggest m

Re: [gmx-users] orca and Segmentation fault

Dear xi zhao, In your case GMX is applying threading and thus not only a single QM job is requested, but eight. You should run mdrun with -nt 1. Then GMX uses only one single CPU and ORCA is called only once (but can be used in parallel). Hope that helps, Christoph On 11/14/2011 10:34 AM, xi

[gmx-users] Could g_order be used to calculate the order parameters for the two bonds C1'-H1', C3'-H3' in DNA?

Dear all, Recently, I have performed simulation on a B-DNA using gromacs, and I want to use g_order in gromacs to get the order parameters for the bonds C1'-H1', C3'-H3'. Is it possible to obtain order parameters for these two bonds with g_order? If possible, Would you please tell me the correct w

Re: [gmx-users] orca and Segmentation fault

./configure --without-qmmm-orca --without--qmmm-gaussian --enable-mpi make make install I installed  gromacs with Parallel  mode,  is not threading. when I run  " mpirun -np 1 mdrun_dd -v -s pyp.tpr&" or mdrun_dd -nt 1 -v -s pyp.tpr it still" Back Off! I just backed up md.log to ./#md.log.20#

RE: [gmx-users] Potential Energy Landscape

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 21 October 2011 13:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Potential Energy Landscape Natalie Stephenson wr

Re: [gmx-users] Atomtype 'CR' not found

On 14/11/2011 9:08 PM, radhika jaswal wrote: Hiii All... I want to do steepest descent energy minimization for molecule Bromobenzisoxazolone Barretin, I have all the required files like.itp and .gro. Also, changed force field from ffG43a1 to ffgmx but no use. Same error of Atomtype 'CR' not f

[gmx-users] Re: orca and Segmentation fault (xi zhao)

THe error message is clear: your spin multiplicity is 0, which is impossible. Please make sure you understand the basics of electronic structure theory. To test this, you can run the QM system only in stand along QM package. gerrit 2. Re: orca and Segmentation fault (xi zhao) 3. RE

Re: [gmx-users] Problem about simulation at high temperature and ratio of sencondary stuctures

On 14/11/2011 8:33 PM, ??? wrote: Hi Gromacs users, I am using GROMACS (ver4.5.3) to run molecular dynamics (MD) simulation. However during my simulation runs, I encountered some problems as stated below: 1. In NPT condition, the box size undergoes changes, especially at high temperature s

[gmx-users] mpirun with remd

dear teacher, when i do remd ,i use the commond : mpirun n8,8,8,8,9,10,15,16,16,20,20,22 -np 24 /export/software/bin/mdrun_mpi_4.5.5 -multidir ./0/ ./1/ ./2/ ./3/ ./4/ ./5/ ./6/ ./7/ ./8/ ./9/ ./10/ ./11/ -replex 1000 -nice 0 -s pmma.tpr -o md -c after_md -pd -table table.xvg -tableb table.xvg -v

Re: [gmx-users] mpirun with remd

On 15/11/2011 12:22 AM, 杜波 wrote: dear teacher, when i do remd ,i use the commond : mpirun n8,8,8,8,9,10,15,16,16,20,20,22 -np 24 /export/software/bin/mdrun_mpi_4.5.5 -multidir ./0/ ./1/ ./2/ ./3/ ./4/ ./5/ ./6/ ./7/ ./8/ ./9/ ./10/ ./11/ -replex 1000 -nice 0 -s pmma.tpr -o md -c after_md -pd

Re: [gmx-users] GROMACS/ORCA QMMM

Dear Jose, I tried oniom which stopped for me either (although without a segfault). Have you tried "QMMMscheme normal"? Christoph On 11/11/2011 05:53 PM, Jose Tusell wrote: Dear GROMACS users, I'm trying to run a QM-MM optimization. I solvate my protein and add ions then I do a classical o

[gmx-users] The equilibrium before REMD simulations

Dear GMX users, I am puzzled about some technical details regarding to the REMD simulation and eager for your generous help. With the purpose to explore the additional conformational space of the protein, I want to employ the REMD method in Gromacs. However, I noticed that in almost all of t

Re: [gmx-users] The equilibrium before REMD simulations

ÏéÇ« ¿× wrote: Dear GMX users, I am puzzled about some technical details regarding to the REMD simulation and eager for your generous help. With the purpose to explore the additional conformational space of the protein, I want to employ the REMD method in Gromacs. However, I noticed that in alm

[gmx-users] Units of Buckingham potential

Hi dear all, For Buckingham potential， there is three parameters A B C In GMX, the units of A B C is the kJ/mol, nm, kJ/mol*nm^6， am I right? Best XJ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Re: [gmx-users] Units of Buckingham potential

On 15/11/2011 2:00 AM, xiaojing gong wrote: Hi dear all, For Buckingham potential， there is three parameters A B C In GMX, the units of A B C is the kJ/mol, nm, kJ/mol*nm^6， am I right? Manual section 2.2 defines the units, and 4.1.2 defines the functional form. Mark -- gmx-users mailing list

Re: [gmx-users] The equilibrium before REMD simulations

Dear Justin, Thanks for your prompt reply! As you say, we should equilibrium each replica at its initial target temperature. So i guess we may do the followings: First, after the minimization and heating, we use NPT to equilibrium the density of the system. And then with the same initial sys

Re: [gmx-users] The equilibrium before REMD simulations

ÏéÇ« ¿× wrote: Dear Justin, Thanks for your prompt reply! As you say, we should equilibrium each replica at its initial target temperature. So i guess we may do the followings: First, after the minimization and heating, we use NPT to equilibrium the density of the system. And then with the same

Re: [gmx-users] Units of Buckingham potential

Many thanks for reply. Another question, If I use Buckingham potential for CNT, and I want to simulate CNT and water, shall I also transfer the SPC.itp from LJ to Buckingham potential? Best XJ 2011/11/14 Mark Abraham > On 15/11/2011 2:00 AM, xiaojing gong wrote: > >> Hi dear all, >> For Buckingh

Re: [gmx-users] The equilibrium before REMD simulations

On 15/11/2011 2:50 AM, ÏéÇ« ¿× wrote: Dear Justin, Thanks for your prompt reply! As you say, we should equilibrium each replica at its initial target temperature. So i guess we may do the followings: First, after the minimization and heating, we use NPT to equilibrium the density of the s

Re: [gmx-users] No locks available.

Hi, On Mon, Nov 14, 2011 at 2:15 AM, lina wrote: > On Mon, Nov 14, 2011 at 7:47 AM, Roland Schulz wrote: > > Hi, > > what file system is this? What operating system on the compute node? In > case > > it is a network file system what file system is used underneath and what > > operating system i

[gmx-users] the force constant in constant speed umbrella pulling

Hi everyone, I am just wondering about the mathematical and physical meaning of this force constant when pulling a ligand from its receptor. So I can imagine a dummy atom is linked to the ligand via a spring, and it is moving away from the receptor at 1 nm/ns with the spring force constant 1000 k

[gmx-users] UNK not found in residue topology

Hello, I'm getting an UNK not found in residue topology error message. After I run pdb2gmx -f XXX.pdb -o conf.pdb Fatal error: Residue 'UNK' not found in residue topology database I figured out what the error was and tried to add UNK as carbon to ffopslaa.rtf [UNK] [ atoms ] UNK

[gmx-users] GMX to remove clashes?

Hi, all, I am wondering if Gromacs can do the following work? Assuming I have a pdb file of an RNA molecule. Some atoms may be too close or even overlap, I am wondering if Gromacs can move the atoms to reasonable positions and remove the bad contacts? The final structure is supposed to be the "mos

Re: [gmx-users] GMX to remove clashes?

Liu, Liang wrote: Hi, all, I am wondering if Gromacs can do the following work? Assuming I have a pdb file of an RNA molecule. Some atoms may be too close or even overlap, I am wondering if Gromacs can move the atoms to reasonable positions and remove the bad contacts? The final structure is

Re: [gmx-users] UNK not found in residue topology

Janowicz, Adrianna C. wrote: Hello, I'm getting an UNK not found in residue topology error message. After I run pdb2gmx -f XXX.pdb -o conf.pdb Fatal error: Residue 'UNK' not found in residue topology database I figured out what the error was and tried to add UNK as carbon to ffopslaa.r

Re: [gmx-users] GMX to remove clashes?

This is a "reasonable" answer :) Thanks for that, and I just tried Gromacs for minimization, and looks the final structure does not have clashes anymore, and also are very close to the initial structure. Another question is if there is a way to add ions automatically, meaning no need to check the

Re: [gmx-users] GMX to remove clashes?

Liu, Liang wrote: This is a "reasonable" answer :) Thanks for that, and I just tried Gromacs for minimization, and looks the final structure does not have clashes anymore, and also are very close to the initial structure. Another question is if there is a way to add ions automatically, mea

Re: [gmx-users] GMX to remove clashes?

Thanks. Do you know how to use a new force field, not amber or charm, but a force field built by someone else, and it's already in Gromacs format (tons of xvg file, right?) On Mon, Nov 14, 2011 at 4:13 PM, Justin A. Lemkul wrote: > > > Liu, Liang wrote: > >> This is a "reasonable" answer :) >>

Re: [gmx-users] GMX to remove clashes?

Liu, Liang wrote: Thanks. Do you know how to use a new force field, not amber or charm, but a force field built by someone else, and it's already in Gromacs format (tons of xvg file, right?) Force fields are not in .xvg format, unless you're talking about using tabulated potentials. In

[gmx-users] import force field

I have a serial of tabulated potentials with the name of *.xvg, which are the function of atom distance. I am wondering how to use them in gromacs simulation? Will that replace the force field, e.g. amber03? Thanks. -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lis

RE: [gmx-users] Time unit issue with g_anaeig

Hi Mark, I ran gmxcheck and it returned the following output: Checking file 1-21.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 7764 Reading frame 49000 time 4900.000 Item#frames Timestep (ps) Step 499840.1 Time 49984

[gmx-users] Query on restraining center of mass of a protein

Hi,   I have a system containing water and a large protein. In the simulation, I do not want the protein center of mass to drift away. I was wondering what will be the reasonable method in gromacs to fix the position of the center of mass of the protein in its original position . I was thinking

RE: [gmx-users] Time unit issue with g_anaeig

Hi again, I just found the solution to the problem. Using trjconv to specify the timestep seems to have helped. Thanks again for the help. Regards, Kei From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Kei Sit Sent: Tuesday, 15 November 2011 9:20 AM To: Di

Re: [gmx-users] Query on restraining center of mass of a protein

On 15/11/2011 10:21 AM, Sanku M wrote: Hi, I have a system containing water and a large protein. In the simulation, I do not want the protein center of mass to drift away. Why do you want it not to drift away? There's nothing magical about the center of a periodic simulation cell. Why do yo

Re: [gmx-users] import force field

On 15/11/2011 9:33 AM, Liu, Liang wrote: I have a serial of tabulated potentials with the name of *.xvg, which are the function of atom distance. I am wondering how to use them in gromacs simulation? Will that replace the force field, e.g. amber03? Thanks. There are sections in the manual that

[gmx-users] Questionable van der waals volumes from g_sas

Hello gmx-users I have been attempting to obtain van der Waal's volumes using the g_sas utility. The command I use to do so is something like g_sas -f hexane.gro -s topol.tpr -probe 0 -tv V_vdw.xvg This seems to give reasonable results for most of my test systems, however when I run the comma

Re: [gmx-users] The equilibrium before REMD simulations

Thanks for everyone's prompt reply! However, i still puzzled why we should use NVT rather than NPT in REMD simulation. As we know that isothermal-isobaric ensemble may be more relevant to the realistic experimental conditions. If the highest temperature was no more than 400K ( i think it is not

Re: [gmx-users] The equilibrium before REMD simulations

On 15/11/2011 11:55 AM, ÏéÇ« ¿× wrote: Thanks for everyone's prompt reply! However, i still puzzled why we should use NVT rather than NPT in REMD simulation. As we know that isothermal-isobaric ensemble may be more relevant to the realistic experimental conditions. If the highest temperature w

[gmx-users] RE: Questionable van der waals volumes from g_sas

Sorry, ignore my last post, only just realised you had set your probe to 0 radius. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304

[gmx-users] RE: Questionable van der waals volumes from g_sas

Jake, Wont the volume be a function of the probe radius that is used? And hence, if it is too big to fit through the ring, the volume will be larger than if the chain was straight? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Mon

Re: [gmx-users] No locks available.

On Mon, Nov 14, 2011 at 7:47 AM, Roland Schulz wrote: > Hi, Well, thanks, here comes the questions you asked before. > what file system is this? What operating system on the compute node? In case > it is a network file system what file system is used underneath and what > operating system is the

[gmx-users] how to select option for genion command automatically?

I am wondering if there is a flag to make the command select SOL automatically instead of pressing some number each time? I have thousands of structures, it is really time-consuming to select one by one. -- Best, Liang Liu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.o

Re: [gmx-users] how to select option for genion command automatically?

Liu, Liang wrote: I am wondering if there is a flag to make the command select SOL automatically instead of pressing some number each time? I have thousands of structures, it is really time-consuming to select one by one. Yes, there is: http://www.gromacs.org/Documentation/How-tos/Using_C

Re: [gmx-users] how to select option for genion command automatically?

This is what you are looking for: http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts?highlight=scripting Terry On Tue, Nov 15, 2011 at 11:42 AM, Liu, Liang wrote: > I am wondering if there is a flag to make the command select SOL > automatically instead of pressing some nu

Re: [gmx-users] how to select option for genion command automatically?

Yes, I found it. THanks. On Mon, Nov 14, 2011 at 9:45 PM, Terry wrote: > > This is what you are looking for: > > > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts?highlight=scripting > > Terry > > > On Tue, Nov 15, 2011 at 11:42 AM, Liu, Liang wrote: > >> I am wondering i

Re: [gmx-users] Positive potential energy for TFE solvent

Hi I am still stuck with same problem of obtaining positive potential energy. >>On 11/11/2011 5:07 PM, Harpreet Basra wrote: >> Hi >> >> I am trying to generate an equilibrated box of 216 TFE molecules.To >> generate the 216 TFE molecule box i performed following steps: > >A suggested workflow c

Re: [gmx-users] Positive potential energy for TFE solvent

On 15/11/2011 6:06 PM, Harpreet Basra wrote: Hi I am still stuck with same problem of obtaining positive potential energy. >>On 11/11/2011 5:07 PM, Harpreet Basra wrote: >> Hi >> >> I am trying to generate an equilibrated box of 216 TFE molecules.To >> generate the 216 TFE molecule box i perfor

[gmx-users] Re: Positive potential energy for TFE solvent

hi, I am still stuck with same problem of obtaining positive potential energy. >>On 11/11/2011 5:07 PM, Harpreet Basra wrote: >> Hi >> >> I am trying to generate an equilibrated box of 216 TFE molecules.To >> generate the 216 TFE molecule box i performed following steps: > >A suggested workflow c