Hi All
I have one PDB structure which I want to use as reference for rmsd
calculation (with best fitting). But I realize in my gromacs trajectory the
same structure (if written in PDB) has different sequence of atoms and some
different atom names (especially H, OP1 vs O1P and O2P vs OP2) compared
Hi All
I have some pdb file and I removed hydrogens. When I try to make ndx file
using some residue option then rather printing atom numbers in that residue
it prints line number where that residue starts and ends.
make_ndx -f no_H.pdb -o test.ndx
selecting as:
r 300-330
Then in ndx file I get
g. if you use r 2
then it complains that residue is missing but I think atom numbers are not
read from 'atom number column' itself but as line numbers
On Fri, Sep 19, 2014 at 9:37 PM, Justin Lemkul wrote:
>
>
> On 9/19/14 8:43 AM, gromacs query wrote:
>
>> Hi All
>>
n such case.
best regards
On Fri, Sep 19, 2014 at 10:20 PM, Justin Lemkul wrote:
>
>
> On 9/19/14 5:15 PM, gromacs query wrote:
>
>> Hi Justin
>>
>> Hope it makes sense now :) Here is the link (small piece of some pdb
>> without hydrogens)
>>
>>
Hi All,
I am trying to split my trajectory in single frame pdbs for some analysis
using trjconv but it ends with an error after ouput 1019 pdbs. I tried with
different version of gromacs (4.6.3 and 5.0) its the same error.
trjconv -s ../em.tpr -f ../image_fitted.trr -o test.pdb -split 10 -b 4
Dear All,
I combined the splitted trajectories (trr) from 50ns to 100ns and got
combined trajectoty trr file. I am wondering whether the new combined
trajectory will start from 0ns or it will retain time/frame information
which 50ns in this case?
Thanks
JIom
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Gromacs Users mailing list
* Plea
ems no more supported)
Thanks
On Mon, Dec 8, 2014 at 3:36 PM, Mark Abraham
wrote:
> Hi,
>
> That depends which tool you used, how you used it, etc. You should use gmx
> check and perhaps gmx dump to see what is there.
>
> Mark
>
> On Mon, Dec 8, 2014 at 4:31 PM, gromacs
Hi All,
I have some amino-acid residue in which some extra side chain(s) attached
by replacing H from amino-acid. I want to simulate this with CHARMM ff.
Somehow I can choose best bonded params.
But in order to keep integral charge on this modified aminoacid I was
thinking if there is any way to
Hi All,
I am using cgenff to derive parameters for some polymer (A-...-C). The
repeating block B has some Oxygen O atom which joins the next residue
(-BO-). When I derive charges for B residue with cgenff then I get net -1
charge on B residue because of this unsatsified O atom. I want to keep
al.
best regards,
Vishal
On Fri, Dec 11, 2015 at 4:43 PM, Justin Lemkul wrote:
>
>
> On 12/11/15 10:17 AM, gromacs query wrote:
>
>> Hi All,
>>
>> I am using cgenff to derive parameters for some polymer (A-...-C). The
>> repeating block B has some Oxyg
caps in topology will give non-integral charge or in other
words this part -CO-CH(X)-NH- will always be non-integral. Sorry am
confused.
Thanks
On Fri, Dec 11, 2015 at 5:50 PM, Justin Lemkul wrote:
>
>
> On 12/11/15 12:17 PM, gromacs query wrote:
>
>> Hi Justin
>>
>>
c 11, 2015 at 6:33 PM, Justin Lemkul wrote:
>
>
> On 12/11/15 1:28 PM, gromacs query wrote:
>
>> Hi Justin
>>
>> I am bit lost I think. For e.g. in the amino acid residues library we have
>> -CO-CH(R)-NH- which we can combine these amino acids in any way and in t
have tried different combinations but this is the minimal formal charge I
was able to achieve.
Thanks again for help.
On Fri, Dec 11, 2015 at 7:23 PM, Justin Lemkul wrote:
>
>
> On 12/11/15 2:20 PM, gromacs query wrote:
>
>> Hi Justin
>>
>> Thanks for the explana
Due to reasons, would it be possible for you to suggest off-list? I will
really appreciate.
Thanks.
On Sat, Dec 12, 2015 at 6:35 PM, Justin Lemkul wrote:
>
>
> On 12/12/15 1:25 PM, gromacs query wrote:
>
>> Hi Justin
>>
>> Somehow I can not use available units in
Hi,
Am wondering how you can have an 'axis' for single stranded DNA
simulation? ssDNA should collapse quickly if starting from helical type
configuration unless you are considering only one strand from ds-DNA or
some restraints or very small ss fragment. If you are using RDF then I
assume your si
Hi All
I have a modified base in normal DNA chain. Thus I added that residue in
rtp file and updated residuetypes.dat as well (CHARMM36). When I use pdb2mx
with -ter interactive mode then it wrongly identifies the ending terminal
at the residue just before the modified base. e.g.
:
:
TER
DC (169
Ah! Thanks Justin, I just need extra coffee. Required file was not in
working directory.
On Sun, Dec 20, 2015 at 9:17 PM, Justin Lemkul wrote:
>
>
> On 12/20/15 4:13 PM, gromacs query wrote:
>
>> Hi All
>>
>> I have a modified base in normal DNA chain. Thus I add
Hi All
I have protein-membrane system and gromacs tutorial by Justin suggests to
do COM separately for protein_membrane and water. I am bit meesed up COM
removal understanding.
1) I want to do diffusion analysis of protein in a membrane (2D/3D) how it
will influence my results if I perform it o
>> It is not a matter of resetting positions; it is about subtracting
falsely accumulated kinetic energy.
Thanks, this is it :)
On Mon, Dec 28, 2015 at 8:58 PM, Justin Lemkul wrote:
>
>
> On 12/28/15 10:28 AM, gromacs query wrote:
>
>> Hi All
>>
>>
>>
Hi All,
I am using charmm36 downloaded from (MacKerell website). Somehow I was
enlightened while reading some papers applying NBFIX by Roux et al. I can
see there is indeed a nbfix.itp file in CHARMM36 (not 27) and used as
default (via forcefield.itp) but the file does not mention any reference
wh
PM, Justin Lemkul wrote:
>
>
> On 6/20/16 12:30 PM, gromacs query wrote:
>
>> Hi All,
>>
>> I am using charmm36 downloaded from (MacKerell website). Somehow I was
>> enlightened while reading some papers applying NBFIX by Roux et al. I can
>> see there is i
ne-protein simulations.
Thanks for any suggestions.
JIomm
On Mon, Jun 20, 2016 at 6:23 PM, Justin Lemkul wrote:
>
>
> On 6/20/16 1:19 PM, gromacs query wrote:
>
>> Thanks Justin, basically am stuck with an old question of using high salt
>> conc. with membrane simulations a
Hi Justin
>> Follow the analysis of the Venable paper
I think you mean this paper: http://pubs.acs.org/doi/abs/10.1021/jp401512z
JIomm
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Hi All,
I have membrane thickness along Z and want to merge peptide in membrane. I
need to translate peptide (say 10 Angs) along -Z to adjust its position and
used command like this:
editconf -f pep.pdb -c -princ -rotate 0 90 0 -translate -10 0 0 -o
new_pep.pdb
It seems that it does not move at
your
> editconf command.
> Your command seems to translate along x.
>
> Chandan
>
> On Mon, Mar 2, 2015 at 5:16 PM, gromacs query
> wrote:
>
> > Hi All,
> >
> > I have membrane thickness along Z and want to merge peptide in membrane.
> I
> > nee
Hi Justin,
>> If that doesn't work, trjconv can translate
Thanks a lot, trjconv works fine. For some reason I could not achieve this
with editconf.
regards,
JIom
On Mon, Mar 2, 2015 at 1:48 PM, Justin Lemkul wrote:
>
>
> On 3/2/15 6:46 AM, gromacs query wrote:
>
Hi,
I am using g_membed (for CG) to insert peptide with following steps:
1) grompp generates a tpr file; with no issues
2) g_membed generates membed.dat; no issues
3) lastly mdrun gives this error:
gmx_mtop_atomlookup_settle_init called without settles
Justin has suggested this may arise due
Hi All,
I am doing CG membrane with protein. After running long simulation I am
getting this error:
Fatal error:
2 of the 13319 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.4 nm) or the two-body cut-off distanc
5 at 5:23 PM, Mark Abraham
wrote:
> Hi,
>
> Very likely your run is blowing up from (long-time) instability - two atoms
> have moved some crazy amount. You can probably confirm that from the time
> series of some observables.
>
> Mark
>
> On Mon, Mar 9, 2015 at 12:54 PM,
Dear All,
mdrun is not giving any error about missing cpt file. It runs using tpr
from initial time zero. Sometimes my job get killed and I need to use cpt
file in some script but if cpt is not found my job starts running from zero
time in tpr file which is harmful as it consumes my processors to
e names as such without any
compromise.
regards,
Jiom
On Wed, Apr 29, 2015 at 12:36 PM, Mark Abraham
wrote:
> On Wed, Apr 29, 2015 at 1:20 PM Kutzner, Carsten wrote:
>
> > Hi JIom,
> >
> > > On 29 Apr 2015, at 11:50, gromacs query
> wrote:
> > >
>
Hi All
I am doing PCA and its working fine if I choose few atoms only (heavy) and
I get extreme pdb file having heavy atoms for, say, eigenvector 1. But I
want to have extremes of all-atom structures, so I thought of doing PCA on
all-atoms but I end up with having Segmentation default error which
; Tsjerk
>
> On Mon, May 11, 2015 at 10:32 PM, gromacs query
> wrote:
>
> > Hi All
> >
> > I am doing PCA and its working fine if I choose few atoms only (heavy)
> and
> > I get extreme pdb file having heavy atoms for, say, eigenvector 1. But I
> > want t
erk Wassenaar
wrote:
> Hi Jio,
>
> You'll have to look at the projections (-proj), and see at which time these
> have an extreme value.
>
> Cheers,
>
> Tsjerk
>
> On Mon, May 11, 2015 at 11:00 PM, gromacs query
> wrote:
>
> > Hi Tsjerk
> >
> &g
re not
> real structures. But you wanted the corresponding all-atom ones.
>
> Cheers,
>
> Tsjerk
> On May 12, 2015 00:45, "gromacs query" wrote:
>
> > Hi Tsjerk
> >
> > In -proj plot of v1 vs Time I used extreme values of V1 and saw
> structures
>
Hi All
I want to align small residues based on 3 atom names only (ignoring rest of
the atoms) and confrms does not require same number of atoms: first.pdb
with 7 atoms and second.pdb with 3 atoms.
echo "0" "0"| gmx confrms -f1 first.pdb.pdb -f2 second.pdb -no -name -o
fit.pdb
I am getting error
Hi All
Am just thinking if my mail was spammed.
Thanks for any help.
On Mon, Jun 22, 2015 at 4:58 PM, gromacs query
wrote:
> Hi All
>
> I want to align small residues based on 3 atom names only (ignoring rest
> of the atoms) and confrms does not require same number of atoms: firs
Hi All,
I have linear polymer in octahedron box and when I try to visualise a
polymer in octahedraon box then water octahedron box looks as expected but
my polymer looks broken.
trjconv_avx -f input.xtc -o out.xtc -pbc mol -ur compact -s input.tpr -b
10
I have tried to use -center (whole po
Hi Victor,
With 'pbc whole' polymer remains broken in pbc and the octahedron box looks
weird too.
JIom
On Thu, Oct 1, 2015 at 2:52 PM, Victor Rosas Garcia
wrote:
> Have you tried the option "-pbc whole" instead of "-pbc mol"?
>
> Victor
>
> 2015-
Hi,
I think its solved, I used -center option but now rather selecting full
polymer I selected some of the central residue in polymer chain. Now box
looks good and polymer is not broken.
JIom
On Thu, Oct 1, 2015 at 3:43 PM, gromacs query
wrote:
> Hi Victor,
>
> With 'pbc
Thanks Justin, your inputs are really helpful. I did basic analysis on
thickness which increased slightly with salt conc. (with NBFix) but I do
need to see other things more carefully.
JIomm
On Tue, Jun 21, 2016 at 12:28 PM, Justin Lemkul wrote:
>
>
> On 6/21/16 6:29 AM, gromacs qu
Hi All,
{apologies if posted multiple times; seems like some trouble with my
account}
I want to pull linear molecule across the membrane in two ways allowing:
- translation along Z and rotation around Z
- translation along Z and rotation in all axes
My current mdp-setting pulls molecular along Z
Hi all,
I would like my perl script to analyse xtc trajectory file directly instead
of analysing human readable extracted frame files (pdb/gro etc.) to save
disk space. I could not find much on mailing list but there was a brief
reference about using Swig which I could not understand how to start
t; files, or using the GROMACS C++ analysis tools template, rather than
> wasting time writing your own code to read them. If you really must, then
> you should wrap this library
> http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library.
>
> Mark
>
> On Fri, Jun
Hi All,
I am using 'equivalent' mdp settings for pull run in Gromacs 4.6 and 2016.
With gromacs 4.6 I get time, 0Z and 1dZ; which I can understand as
explained here: https://www.mail-archive.com/gmx-users@gromacs.org/
msg22453.html
With Gromacs 2016 I get only time and some distance and xvg fil
Hi All,
Am just wondering if somebody has seen this in different gmx versions?
Thanks.
JIom
On Fri, Aug 25, 2017 at 11:00 AM, gromacs query
wrote:
> Hi All,
>
> I am using 'equivalent' mdp settings for pull run in Gromacs 4.6 and 2016.
>
> With gromacs 4.6 I get time
Hi All,
I have some issues with gromacs performance. There are many nodes and each
node has number of gpus and the batch process is controlled by slurm.
Although I get good performance with some settings of number of gpus and
nprocs but when I submit same job twice on the same node then the
perfor
Sorry forgot to add; we thought the two jobs are using same GPU ids but
cuda visible devices show both jobs are using different ids (0,1 and 2,3)
-
J
On Wed, Sep 13, 2017 at 5:33 PM, gromacs query
wrote:
> Hi All,
>
> I have some issues with gromacs performance. There are many nodes
t; --
> Szilárd
>
>
> On Wed, Sep 13, 2017 at 6:35 PM, gromacs query
> wrote:
> > Sorry forgot to add; we thought the two jobs are using same GPU ids but
> > cuda visible devices show both jobs are using different ids (0,1 and 2,3)
> >
> > -
> > J
>
your mdrun launch command.
>
>
> I hope one of these will deliver the desired results :)
>
> Cheers,
> --
> Szilárd
>
>
> On Wed, Sep 13, 2017 at 7:47 PM, gromacs query
> wrote:
> > Hi Szilárd,
> >
> > Thanks for your reply. This is useful but now am think
iably less
than 50%) as expected from a single independent job. Now am wondering if
its still related to overlap of cores as pin on should lock the cores for
the same job.
-J
On Wed, Sep 13, 2017 at 7:33 PM, gromacs query
wrote:
> Hi Szilárd,
>
> Thanks, option 3 was in my mind but I need
a node?
>
> How many threads/cores does you node have? Can you share log files?
>
> Cheers,
> --
> Szilárd
>
>
> On Wed, Sep 13, 2017 at 9:14 PM, gromacs query
> wrote:
> > Hi Szilárd,
> >
> > Sorry I was bit quick to say its working with pinoffset. I j
M, Szilárd Páll
wrote:
> On Wed, Sep 13, 2017 at 11:14 PM, gromacs query
> wrote:
> > Hi Szilárd,
> >
> > Thanks again. I tried now with -multidir like this:
> >
> > mpirun -np 16 gmx_mpi mdrun -s test -ntomp 2 -maxh 0.1 -multidir t1 t2
> t3 t4
> >
&g
t convenient
> sometimes when job crashes in the middle and automatic restart from cpt
> file would be difficult.
>
> -J
>
>
> On Thu, Sep 14, 2017 at 11:26 AM, Szilárd Páll
> wrote:
>
>> On Wed, Sep 13, 2017 at 11:14 PM, gromacs query
>> wrote:
>> > Hi S
Hi All,
Though am naive, and much appreciate the efforts required to put things
altogether but I think I found few things confusing or wrong by mistake or
repeated here:
http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html
The replaced corrections are in [CAPITAL] (plea
Hi Szilárd,
{I had to trim the message as my message is put on hold because only 50kb
allowed and this message has reached 58 KB! Not due to files attached as
they are shared via dropbox}; Sorry seamless reading might be compromised
for future readers.
Thanks for your replies. I have shared log f
Hi Qinghua,
I am not sure about any too but If you have pdb working fine with AMBER
(as you said) then its not much of work doing it 'manually' ; takes less
than two minutes. You can do this:
1) First remove hydrogens and let gromacs add by itself at the final step
(matching from charm36). You c
and how to lay out jobs in a node to
> get best throughput. Start with run configs testing settings with
> -multi to avoid pinning headaches and fill at least half a node (or a
> full node) with #concurrent simulations >= #GPUs.
>
I will see if I get some node free. I need to wait.
Th
Dear All
I never used Gromacs for nucleic acids. In AMBER there is ff10
(ff99SB+parmbasco+ also one needs to add ions according to water used by
Thomas Cheatham et al.)
does gromacs include this force field (AMBER ff implemented in gromacs)?
regards
JIo
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Gromacs Users mailing list
* Please s
Dear All
I want to simulate two polymer chains as rigid bodies, in other words
allowing two polymer to interact with each other but keeping their internal
coordinates restrained. Also it can be seen as two rods interacting with
each other.
Which flags/options can be used in Gromacs?
regards
JIom
ilárd Páll wrote:
> >>
> >> Hi,
> >>
> >> If you look at share/gromacs/top/ in the GROMACS installation
> >> directory you can see which FF-s are included and amberff10 is not
> >> there, so the answer is no.
> >>
> >> Cheers,
LINCS or SHAKE (all atoms) can be used for this?
or some better options available? it can be seen as two protein helix
interacting with each other as rigid bodies...
thanks
On Wed, Nov 27, 2013 at 12:35 AM, gromacs query wrote:
> Dear All
>
> I want to simulate two polymer chains
Hi All
I have built DNA with NAB in AMBER and it provide names as D*, D*3, D*5
(where * = A,T,G,C) and want to use charmm27 in gromacs. The
charmm27.ff/dna.rtp does not have D*5 or D*3 and has only D* residues, so I
renamed D*5 or D*3 to just corresponding D* residues. The output pdb with
pdb2gmx
d use some .top file? (and if I understood it correctly; if I am using
from rtp file, which is a sort of residue library file, then order does NOT
matter)
thanks
On Tue, Feb 4, 2014 at 5:03 PM, Justin Lemkul wrote:
>
>
> On 2/4/14, 11:50 AM, gromacs query wrote:
>
>> Hi All
>
some common top file then even I can not
use same .top file?
On Tue, Feb 4, 2014 at 5:39 PM, Justin Lemkul wrote:
>
>
> On 2/4/14, 12:35 PM, gromacs query wrote:
>
>> Hi Justin
>>
>> Presence of the correct atoms is the only absolute requirement
>>>>
&g
Hi All
I have simple DNA pdb which has just 5 DA residues built from NAB in AMBER.
I am trying to use pdb2gmx with charmm36-jan2014.ff downloaded from:
http://mackerell.umaryland.edu/CHARMM_ff_params.html
pdb2gmx -f a.pdb -o gro.pdb -ff charmm36-jan2014
I have changed all names according to
Hi Justin
Thanks it worked, just to add I have to use -ignh as well. I think it does
not detect some H at 5 end built from AMBER NAB programme.
Jiom
On Wed, Feb 5, 2014 at 3:13 PM, Justin Lemkul wrote:
>
>
> On 2/5/14, 9:49 AM, gromacs query wrote:
>
>> Hi All
>>
Hi All
I am trying to use charmm36 (charmm36-jan2014 from charmm website) with
popc membrane built using charmm-gui (have water and ions).
I used commands as follows:
pdb2gmx -f step5_assembly.pdb -o popc.gro -water tip3p -ff charmm36-jan2014
editconf -f popc.gro -o popc_box.gro -c -d 0.0
grompp
error.
On Mon, Mar 3, 2014 at 5:46 PM, Justin Lemkul wrote:
>
>
> On 3/3/14, 10:57 AM, gromacs query wrote:
>
>> Hi All
>>
>> I am trying to use charmm36 (charmm36-jan2014 from charmm website) with
>> popc membrane built using charmm-gui (have water and ion
and trying, will let you know; I am newbie to
gromacs)
thanks
On Mon, Mar 3, 2014 at 6:48 PM, Mark Abraham wrote:
> On Mon, Mar 3, 2014 at 7:25 PM, gromacs query >wrote:
>
> > Hi Justin
> >
> > Its problem with the waters I think.
>
>
> Can't be, they
t works fine and all Hs are added without error.
thanks
JIom
On Wed, Feb 5, 2014 at 3:53 PM, gromacs query wrote:
> need a coffee!
>
>
> On Wed, Feb 5, 2014 at 3:44 PM, Justin Lemkul wrote:
>
>>
>>
>> On 2/5/14, 10:42 AM, gromacs query wrote:
>>
>&g
Hi Justin
Yes I chose termini 5TER or 3TER correctly but it only works fine when D*5
replaced by D* and D*3 by D* otherwise it ends with errors as said
previously.
thanks
JIom
On Tue, Mar 4, 2014 at 1:00 AM, Justin Lemkul wrote:
>
>
> On 3/3/14, 7:57 PM, gromacs query wrote:
&g
Mar 3, 2014 at 9:07 PM, Justin Lemkul wrote:
>
>
> On 3/3/14, 3:56 PM, gromacs query wrote:
>
>> What atom numbers are on line 184419? What atom types are they in the
>>>>
>>> [atoms] section for that [moleculetype]?
>>
>> These are waters only
Hi all
I have very simple query. While continuing simulations why we need to use
*.gro (-c) with grompp as *.cpt (-t) has all the information (as checked
with gmxcheck)?
cpt file should suffice all the purposes. I tried using grompp providing -t
*.cpt file but without -c *.gro file, it does not wo
Hi All
Though its mentioned here how to restart jobs:
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
but I tried to run something like this (by scripting) but copying here how
script is looping jobs:
#stage 1
grompp -f npt.mdp -c conf_1ns.gro -t state_1ns.cpt -p topol.top -o
Hi Jutsin
Thanks, I was thinking that .cpt has all the information which I assumed
would work like AMBER restart file to read time from .cpt (~ amber restart)
file.
regards
Jiom
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Hi All
I am simulating charmm36 popc membrane with ions and got this error (NPT
with position restraints) before this I did minimization and NVT with
posres.
I could not find "Bond length not finite" error in archive.
Step Time Lambda
00.0
Hi Justin
I reduced dt from 0.002 to 0.001, till now its working fine. I will post
again if get some trouble.
thanks
Jiom
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* Can't post? Read http://www.gro
Hi All
I am using topo writegmxtop output.top in VMD and it writes fake sort of
top file which needs further user based adjustments.
The top file so generated has all [bonds] [angles] [dihedral] information
but [pairs] are missing. I am using charmm36 which says gen-pair =yes in
forcefield.itp.
Hi All
In g_anaeig we have this option -extr: calculate the two extreme
projections along a trajectory
It provides me two pdb files which are extreme (I don't want to use
interpolate -nframes option). I have simple doubt: say if I am doing this
for Eigenvector 1 (EV1) then do these two pdbs simpl
Dear All
I am creating a truncated octahedron box and in vmd it appears as a
rectangular box. In mailing list it has been suggested to use trjconv -ur
compact option. But I have two issues,
1) I get box vector angle 70 90 70 with editconf and should be around 109
109 109 for a truncated octahedro
Hi All
I generated my npt.tpr with:
tinit=0
dt=0.002
nsteps=125000
I am trying to extend simulation for 250 ps like this:
tpbconv_mpi -s npt.tpr -o npt_new.tpr -extend 250
But when I used this npt_new.tpr simulation it ran for 500 ps. Have I
missed something?
Also one more thing why the
:07 PM, Justin Lemkul wrote:
>
>
> On 7/3/14, 6:05 PM, gromacs query wrote:
>
>> Hi All
>>
>> I generated my npt.tpr with:
>>
>>
>> tinit=0
>>
>> dt=0.002
>>
>> nsteps=125000
>>
>> I am trying to extend simu
Hi
forgive my ignorance but I could not find whether my cpt was read
successfully or not as I dont see anything in log file as which files were
taken as input. Or any keyword I should search for?
On Thu, Jul 3, 2014 at 11:36 PM, Justin Lemkul wrote:
>
>
> On 7/3/14, 6:34 PM, grom
2014 at 11:58 PM, Justin Lemkul wrote:
>
>
> On 7/3/14, 6:51 PM, gromacs query wrote:
>
>> Hi
>>
>> forgive my ignorance but I could not find whether my cpt was read
>> successfully or not as I dont see anything in log file as which files were
>>
Hi
Sorry I think I found the error. I was using wrong name of -cpi file. But
its strange that mdrun does not complain even if it could not find the
file and it still ran the job.
On Fri, Jul 4, 2014 at 12:31 AM, gromacs query
wrote:
> Hi Justin
>
> Indeed this key word 'Read
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